Earlier exploration note
How BioProject and BioSample records relate, written before any census. The worked examples still hold; for measured coverage of every route out of a BioProject, see the route matrix.
BioProject Series¶
Overview¶
What are BioProject and BioSample records?¶
NCBI BioProject records describe the umbrella study or research effort, while BioSample records describe the individual biological materials used in that study. A typical workflow starts from a BioProject accession, finds the linked BioSamples, and then follows those samples to related sequencing runs, assemblies, or other submitted data.
Connections to Sequencing Databases¶
BioProject and BioSample accessions act as shared metadata anchors across many sequence and expression repositories. The BioProject groups the overall study, and each BioSample records the biological source material for one or more experiments. Other databases then attach their own records to those same study and sample identifiers.
In NCBI SRA, sequencing records usually sit below BioSample and BioProject
metadata. A BioProject can contain many BioSamples, each BioSample can have one
or more SRA experiments, and each experiment can have one or more sequencing
runs. This lets a user start with a study accession such as PRJNA..., find the
sample accessions such as SAMN..., and then locate the raw read accessions
such as SRR..., SRX..., or SRS....
GEO is often used for expression studies, including RNA-seq and array-based
experiments. GEO records have their own accessions, such as series (GSE...),
samples (GSM...), and platforms (GPL...). For sequencing-based GEO studies,
the GEO series or samples may link out to SRA records, and those SRA records may
then link back to the relevant BioProject and BioSample records. In practice,
GEO often describes the experimental design and processed expression data, while
SRA stores the raw sequencing reads.
ENA is the European nucleotide archive and exchanges many sequence records with
NCBI through the International Nucleotide Sequence Database Collaboration. ENA
uses accessions such as PRJEB... for projects, SAMEA... for samples,
ERX... for experiments, and ERR... for runs. These often correspond to the
same conceptual levels as NCBI BioProject, BioSample, SRA experiment, and SRA
run records, even when the accession prefixes differ.
ArrayExpress, now closely connected with functional genomics data resources at EMBL-EBI, is similar to GEO in that it describes expression experiments and their processed metadata. ArrayExpress studies may point to ENA run or experiment records for raw sequencing data, while array-based studies may remain primarily within ArrayExpress. When the same study is represented in both NCBI and EMBL-EBI systems, BioProject/BioSample-style identifiers help connect the study-level and sample-level metadata to the raw and processed data records.
A common lookup chain is:
BioProject -> BioSample -> SRA/ENA experiment -> SRA/ENA run
GEO series -> GEO sample -> SRA run -> BioSample/BioProject
ArrayExpress experiment -> ENA run/experiment -> sample/project metadata
BioProject database from e-utils API¶
BioProject database is indexed in the e-utils API. This is the latest information about the BioProject database as of 2026-04-21:
{
"header": {
"type": "einfo",
"version": "0.3"
},
"einforesult": {
"dbinfo": [
{
"dbname": "bioproject",
"menuname": "BioProject",
"description": "BioProject Database",
"dbbuild": "Build260421-0620.1",
"count": "1038660",
"lastupdate": "2026/04/21 07:06",
}
]
}
}
We can also look at the fields that are indexed in the BioProject database:
| # | name | fullname | description | termcount | isdate | isnumerical | singletoken | hierarchy | ishidden |
|---|---|---|---|---|---|---|---|---|---|
| 0 | ALL | All Fields | All terms from all searchable fields | 22947927 | N | N | N | N | N |
| 1 | UID | UID | Unique number assigned to publication | 0 | N | Y | Y | N | Y |
| 2 | FILT | Filter | Limits the records | 113 | N | N | Y | N | N |
| 3 | ORGN | Organism | Organism | 1631760 | N | N | Y | Y | N |
| 4 | PRJA | Project Accession | Project Accession | 1318565 | N | N | Y | N | N |
| 5 | TYPE | Project Type | Project Type | 2 | N | N | Y | N | N |
| 6 | STPE | Project Subtype | Project Subtype | 7 | N | N | Y | N | N |
| 7 | DATE | Registration Date | Registration Date | 8509 | Y | N | Y | N | N |
| 8 | TITL | Title | Title | 2569751 | N | N | Y | N | N |
| 9 | CEN | Submitter Organization | Submitter Organization(s) | 177331 | N | N | Y | N | N |
| 10 | ACCN | Replicon accession | Space delimited GenBank or RefSeq Replicon Acc... | 473857 | N | N | Y | N | N |
| 11 | RTYP | Replicon type | Replicon Type | 17 | N | N | Y | N | N |
| 12 | RNME | Replicon name | Replicon Name | 129 | N | N | Y | N | Y |
| 13 | LTP | Locus Tag Prefix | Locus Tag Prefix | 3913133 | N | N | Y | N | N |
| 14 | WORD | Description | Organism/Project Description | 10280547 | N | N | Y | N | N |
| 15 | KWRD | Keyword | Keyword | 439 | N | N | Y | N | N |
| 16 | PROP | Properties | Project/Organism Properties | 50 | N | N | Y | N | N |
| 17 | DTPE | Project Data Type | Project Data Type | 37 | N | N | Y | N | N |
| 18 | GRNT | Grant ID | Grant ID | 64034 | N | N | Y | N | N |
| 19 | FUND | Funding Agency | Funding Agency | 15063 | N | N | Y | N | N |
| 20 | PMID | PMID | Pubmed ID | 211632 | N | Y | Y | N | N |
| 21 | DOID | DOI | DOI ID | 7190 | N | N | Y | N | Y |
| 22 | PID | ProjectID | Project ID | 1038713 | N | Y | Y | Y | N |
| 23 | RELV | Relevance | Relevance | 5061 | N | N | Y | N | N |
| 24 | ANME | Assembly name | Assembly Name | 3368401 | N | N | Y | N | N |
| 25 | BPRJ | BioProject ID | BioProject ID or accession | 2357225 | N | N | Y | N | Y |
| 26 | TPRJ | Top Bioproject | Top Bioproject ID | 64059 | N | Y | Y | N | Y |
| 27 | WGSA | WGS Accession | WGS Accessions | 2095332 | N | N | Y | N | N |
| 28 | AACC | Assembly Accession | Assembly Accession | 2543040 | N | N | Y | N | N |
| 29 | ATNM | Attribute Name | Attribute Name | 6 | N | N | Y | N | N |
| 30 | ATTR | Attribute | Attribute | 209727 | N | N | Y | N | N |
Moreover, we can look at the links that are indexed in the BioProject database:
| # | name | menu | description | dbto |
|---|---|---|---|---|
| 0 | bioproject_assembly_all | Assembly Links | All related Assemblies | assembly |
| 1 | bioproject_bioproject | BioProject | Links from project to related projects | bioproject |
| 2 | bioproject_bioproject_d2u | Umbrella projects | All Umbrella projects | bioproject |
| 3 | bioproject_bioproject_u2d | Data projects | All Data projects | bioproject |
| 4 | bioproject_biosample_all | BioSample Links | All related BioSamples | biosample |
| 5 | bioproject_dbvar | dbVar | Link from BioProjects to dbVar | dbvar |
| 6 | bioproject_gap | dbGaP Links | dbGaP Links | gap |
| 7 | bioproject_gds | GEO DataSet Links | GEO DataSet links | gds |
| 8 | bioproject_genome | Genome Links | Related Genomes | genome |
| 9 | bioproject_nuccore | Nucleotide Links | Related Nucleotide entry | nuccore |
| 10 | bioproject_nuccore_genomic_dna | Genomic DNA | Link to genomic DNA records | nuccore |
| 11 | bioproject_nuccore_genomic_rna | Genomic RNA | Link to genomic RNA records | nuccore |
| 12 | bioproject_nuccore_map | Map Records | Link to map record(s) | nuccore |
| 13 | bioproject_nuccore_reference | Reference Genome Sequences Links | Reference Genome Sequences | nuccore |
| 14 | bioproject_nuccore_repr | Representative Genome Sequences Links | Representative Genome Sequences | nuccore |
| 15 | bioproject_nuccore_transcript | Transcript | Link to transcript records | nuccore |
| 16 | bioproject_nuccore_tsamaster | TSA master | Link to TSA master record(s) | nuccore |
| 17 | bioproject_nuccore_tsatranscript | TSA transcript | Link to TSA transcript record(s) | nuccore |
| 18 | bioproject_nuccore_wgsmaster | WGS master | Link to WGS master record(s) | nuccore |
| 19 | bioproject_nuccore_wgstranscript | WGS transcript | Link to WGS transcript record(s) | nuccore |
| 20 | bioproject_pmc | PMC Links | PMC links | pmc |
| 21 | bioproject_protein | Protein Links | Related Proteins | protein |
| 22 | bioproject_pubmed | PubMed Links | PubMed Links | pubmed |
| 23 | bioproject_snp | SNP Links | Related SNP record | snp |
| 24 | bioproject_sra_all | SRA Links | All related SRA Experiments | sra |
| 25 | bioproject_taxonomy | Taxonomy Links | Taxonomy Links | taxonomy |
Fetching directions from BioProject series¶
We are particularly interested in fetching sequencing data from BioProject and BioSample records. So we will focus on the links to GEO, SRA, ENA and ArrayExpress databases. We have two ways of fetching the data for related databases: by querying those databases directly using the BioProject accession, or by following the links that are indexed in the BioProject database.
It is possible to directly query the following databases using the BioProject accession: - BioProject database itself - GEO datasets - SRA experiments - ENA experiments
It is also possible to follow the links that are indexed in the BioProject database to fetch the related records in those databases. The links that are indexed in the BioProject database include: - GEO datasets linked to the BioProject - BioSamples linked to the BioProject - SRA experiments linked to the BioProject
Direct Querying¶
BioProject database¶
Let's try to fetch the linked GEO datasets and SRA experiments for a specific BioProject. Let's go with PRJNA988806, which is a lung metastasis study in mice. Let's start by searching for the BioProject accession in the BioProject database. e-search query eutils_search(query="PRJNA988806[PRJA]", db=db) will give us the following results:
{
"header": {
"type": "esearch",
"version": "0.3"
},
"esearchresult": {
"count": "1",
"retmax": "1",
"retstart": "0",
"querykey": "1",
"webenv": "MCID_69f375ae0f91922ac904b7db",
"idlist": [
"988806"
],
"translationset": [],
"translationstack": [
{
"term": "PRJNA988806[PRJA]",
"field": "PRJA",
"count": "1",
"explode": "N"
},
"GROUP"
],
"querytranslation": "PRJNA988806[PRJA]"
}
}
We can see that the search returned one result, which is the BioProject with accession. Let's take at look at the summary of this BioProject using eutils_summary:
{
"header": {
"type": "esummary",
"version": "0.3"
},
"result": {
"uids": [
"988806"
],
"988806": {
"uid": "988806",
"taxid": 10090,
"project_id": 988806,
"project_acc": "PRJNA988806",
"project_type": "Primary submission",
"project_data_type": "Transcriptome or Gene expression",
"sort_by_projecttype": 317146,
"sort_by_datatype": 293436,
"sort_by_organism": 418525,
"project_subtype": "",
"project_target_scope": "Multiisolate",
"project_target_material": "Transcriptome",
"project_target_capture": "Whole",
"project_methodtype": "Sequencing",
"project_method": "",
"project_objectives_list": [
{
"project_objectivestype": "Expression",
"project_objectives": ""
}
],
"registration_date": "2023/06/28 00:00",
"project_name": "Aspartate signaling increases the aggressiveness of lung metastases by inducing eIF5A-mediated translation (scRNA-Seq)",
"project_title": "Aspartate signaling increases the aggressiveness of lung metastases by inducing eIF5A-mediated translation (scRNA-Seq)",
"project_description": "Lung metastases are detected in more than half of patients with metastatic tumors. However, it remains largely unknown why the lung environment is a permissive niche for metastases. Here, we discover that pulmonary aspartate triggers a cellular signaling cascade in disseminated cancer cells resulting in a translational program that boosts lung metastasis. Specifically, we observe that patients and mice with breast cancer have high concentrations of aspartate in their lung interstitial fluid. This extracellular aspartate activates the ionotropic N-methyl-D-aspartate (NMDA) receptor in cancer cells, which induces CREB-dependent mRNA expression of deoxyhypusine hydroxylase (DOHH). The latter is essential for hypusination, a posttranslational modification required for the activity of the non-classical translation initiation factor eIF5A. In turn, a translational program with TGF-\u03b2 signaling as a central hub promotes collagen remodeling in the disseminated breast cancer cells. We detect key aspects of this mechanism in lung metastases from patients with breast cancer. In summary, we discover that pulmonary aspartate increases with breast cancer and induces a signaling cascade promoting the growth of lung metastases. Overall design: scRNA-seq from lungs of female BALB/c mice treated with control medium (CM) or medium containing tumor-secreted factors (TSF) for 3 weeks (3 injections per week), and subsequently either euthanized (pre-metastatic niche, CM0/TSF0), or injected i.v. with 25,000 CD90.1-expressing 4T1 cancer cells and then euthanized 11 days (metastatic seeding, CM1/TSF1) or 16 days (metastatic colonization, CM2/TSF2) after cancer-cell injection.",
"keyword": "",
"relevance_agricultural": "",
"relevance_medical": "",
"relevance_industrial": "",
"relevance_environmental": "",
"relevance_evolution": "",
"relevance_model": "Yes",
"relevance_other": "",
"organism_name": "Mus musculus",
"organism_strain": "",
"organism_label": "",
"sequencing_status": "SRA/Trace",
"submitter_organization": "Laboratory of Cellular Metabolism and Metabolic Regulation, VIB-KU Leuven Center for Cancer Biology, VIB/KU Leuven",
"submitter_organization_list": [
"Laboratory of Cellular Metabolism and Metabolic Regulation, VIB-KU Leuven Center for Cancer Biology, VIB/KU Leuven"
],
"supergroup": "Eukaryotes"
}
}
}
From the summary, we can confirm that this BioProject is a transcriptome study of lung metastases in mice. Now we can look at the links that are indexed in the BioProject database.
GEO¶
Let's try querying the GEO database directly using the BioProject accession:
db = "gds"
eutils_search(query="PRJNA988806[ALL]", db=db, api_key=NCBI_API_KEY)
{
"header": {
"type": "esearch",
"version": "0.3"
},
"esearchresult": {
"count": "1",
"retmax": "1",
"retstart": "0",
"querykey": "1",
"webenv": "MCID_6a01e5ad43a484eaba0081ca",
"idlist": [
"200236084"
],
"translationset": [],
"translationstack": [
{
"term": "PRJNA988806[ALL]",
"field": "ALL",
"count": "1",
"explode": "N"
},
"GROUP"
],
"querytranslation": "PRJNA988806[ALL]"
}
}
Great, we can see that there is one GEO dataset linked to this BioProject, with the accession GSE236084. We can fetch the summary of this GEO dataset using eutils_summary:
eutils_summary(
webenv=search_results["esearchresult"]["webenv"],
query_key=search_results["esearchresult"]["querykey"],
db=db,
api_key=NCBI_API_KEY
)
{
"header": {
"type": "esummary",
"version": "0.3"
},
"result": {
"uids": [
"200236084"
],
"200236084": {
"uid": "200236084",
"accession": "GSE236084",
"gds": "",
"title": "Aspartate signaling increases the aggressiveness of lung metastases by inducing eIF5A-mediated translation (scRNA-Seq)",
"summary": "Lung metastases are detected in more than half of patients with metastatic tumors. However, it remains largely unknown why the lung environment is a permissive niche for metastases. Here, we discover that pulmonary aspartate triggers a cellular signaling cascade in disseminated cancer cells resulting in a translational program that boosts lung metastasis. Specifically, we observe that patients and mice with breast cancer have high concentrations of aspartate in their lung interstitial fluid. This extracellular aspartate activates the ionotropic N-methyl-D-aspartate (NMDA) receptor in cancer cells, which induces CREB-dependent mRNA expression of deoxyhypusine hydroxylase (DOHH). The latter is essential for hypusination, a posttranslational modification required for the activity of the non-classical translation initiation factor eIF5A. In turn, a translational program with TGF-\u03b2 signaling as a central hub promotes collagen remodeling in the disseminated breast cancer cells. We detect key aspects of this mechanism in lung metastases from patients with breast cancer. In summary, we discover that pulmonary aspartate increases with breast cancer and induces a signaling cascade promoting the growth of lung metastases.",
"gpl": "24247",
"gse": "236084",
"taxon": "Mus musculus",
"entrytype": "GSE",
"gdstype": "Expression profiling by high throughput sequencing",
"ptechtype": "",
"valtype": "",
"ssinfo": "",
"subsetinfo": "",
"pdat": "2024/10/04",
"suppfile": "TAR, TXT",
"samples": [
{
"accession": "GSM7518067",
"title": "TSF1a, Lungs from TSF Injection, Metastatic Seeding (d11), Replicate a"
},
{
"accession": "GSM7518065",
"title": "CM1, Lungs from CM Injection, Metastatic Seeding (d11)"
},
{
"accession": "GSM7518068",
"title": "TSF1b, Lungs from TSF Injection, Metastatic Seeding (d11), Replicate b"
},
{
"accession": "GSM7518066",
"title": "CM2, Lungs from CM Injection, Metastatic Colonization (d16)"
},
{
"accession": "GSM7518069",
"title": "TSF2, Lungs from TSF Injection, Metastatic Colonization (d16)"
}
],
"relations": [],
"extrelations": [],
"n_samples": 5,
"seriestitle": "",
"platformtitle": "",
"platformtaxa": "",
"samplestaxa": "",
"pubmedids": [
"39743589"
],
"projects": [],
"ftplink": "ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE236nnn/GSE236084/",
"geo2r": "no",
"bioproject": "PRJNA988806"
}
}
}
We can see that the GEO dataset has the same title and summary as the BioProject, and it also has a link to the BioProject accession. Moreover, we can see that there are 5 samples linked to this GEO dataset, with accessions GSM7518067, GSM7518065, GSM7518068, GSM7518066, and GSM7518069.
SRA¶
Let's try doing the same for SRA experiments. We can query the SRA database directly using the BioProject accession:
db = "sra"
eutils_search(query="PRJNA988806[GPRJ]", db=db)
{
"header": {
"type": "esearch",
"version": "0.3"
},
"esearchresult": {
"count": "5",
"retmax": "5",
"retstart": "0",
"querykey": "1",
"webenv": "MCID_6a01e6a1d46d3a12250bba73",
"idlist": [
"28241758",
"28241757",
"28241756",
"28241755",
"28241754"
],
"translationset": [],
"translationstack": [
{
"term": "PRJNA988806[GPRJ]",
"field": "GPRJ",
"count": "5",
"explode": "Y"
},
"GROUP"
],
"querytranslation": "PRJNA988806[GPRJ]"
}
}
We can see that there are 5 SRA experiments linked to this BioProject. We can fetch the summary of these SRA experiments using eutils_summary:
eutils_summary(
webenv=search_results["esearchresult"]["webenv"],
query_key=search_results["esearchresult"]["querykey"],
db=db
)
{
"header": {
"type": "esummary",
"version": "0.3"
},
"result": {
"uids": [
"28241758",
"28241757",
"28241756",
"28241755",
"28241754"
],
"28241758": {
"uid": "28241758",
"expxml": " <Summary><Title>GSM7518069: TSF2, Lungs from TSF Injection, Metastatic Colonization (d16); Mus musculus; RNA-Seq</Title><Platform instrument_model=\"Illumina NovaSeq 6000\">ILLUMINA</Platform><Statistics total_runs=\"1\" total_spots=\"332639939\" total_bases=\"39584152741\" total_size=\"13332204657\" load_done=\"true\" cluster_name=\"public\"/></Summary><Submitter acc=\"SRA1663813\" center_name=\"Laboratory of Cellular Metabolism and Metabolic Re\" contact_name=\"GEO Group\" lab_name=\"\"/><Experiment acc=\"SRX20810436\" ver=\"2\" status=\"public\" name=\"GSM7518069: TSF2, Lungs from TSF Injection, Metastatic Colonization (d16); Mus musculus; RNA-Seq\"/><Study acc=\"SRP446371\" name=\"Aspartate signaling increases the aggressiveness of lung metastases by inducing eIF5A-mediated translation (scRNA-Seq)\"/><Organism taxid=\"10090\" ScientificName=\"Mus musculus\"/><Sample acc=\"SRS18093899\" name=\"\"/><Instrument ILLUMINA=\"Illumina NovaSeq 6000\"/><Library_descriptor><LIBRARY_NAME>GSM7518069</LIBRARY_NAME><LIBRARY_STRATEGY>RNA-Seq</LIBRARY_STRATEGY><LIBRARY_SOURCE>TRANSCRIPTOMIC SINGLE CELL</LIBRARY_SOURCE><LIBRARY_SELECTION>cDNA</LIBRARY_SELECTION><LIBRARY_LAYOUT><PAIRED/></LIBRARY_LAYOUT><LIBRARY_CONSTRUCTION_PROTOCOL>Upon mice euthanasia, lungs were extracted and washed in blood bank saline, dried, and minced for ~ 2 minutes using blades. Minced lung tissues were then incubated with Liberase (0.3 mg/mL) and DNAse1 (1 \u03bcg/mL) for 45 min at 37\u00b0C, with occasional vortexing. The reaction was then quenched with PBS + 3% FBS + 2mM EDTA, after which cells were filtered through a 70\u03bcm cell strainer, washed once, and incubated with Red Blood Cell Lysis buffer. After red blood cell lysis, cells were washed once more and transferred through a 40 \u03bcm cell strainer. Cells were then pooled together from the 3 independent lung dissociations performed per group, resuspended in cell-culture medium at a density of 10^6 cells/mL, and kept on ice for immediate processing into single-cell cDNA libraries. Cell suspensions for each sample were converted to barcoded single-cell cDNA libraries using the Chromium Single Cell 5' v1.1 Library Kit, following the manufacturer's guidelines, and aiming for a total of 10,000 cells per library.</LIBRARY_CONSTRUCTION_PROTOCOL></Library_descriptor><Bioproject>PRJNA988806</Bioproject><Biosample>SAMN36028297</Biosample> ",
"runs": " <Run acc=\"SRR25056225\" total_spots=\"332639939\" total_bases=\"39584152741\" load_done=\"true\" is_public=\"true\" cluster_name=\"public\" static_data_available=\"true\"/> ",
"extlinks": "",
"createdate": "2024/10/04",
"updatedate": "2023/06/28"
},
"28241757": {
"uid": "28241757",
"expxml": " <Summary><Title>GSM7518068: TSF1b, Lungs from TSF Injection, Metastatic Seeding (d11), Replicate b; Mus musculus; RNA-Seq</Title><Platform instrument_model=\"Illumina NovaSeq 6000\">ILLUMINA</Platform><Statistics total_runs=\"1\" total_spots=\"321922508\" total_bases=\"38308778452\" total_size=\"12983749287\" load_done=\"true\" cluster_name=\"public\"/></Summary><Submitter acc=\"SRA1663813\" center_name=\"Laboratory of Cellular Metabolism and Metabolic Re\" contact_name=\"GEO Group\" lab_name=\"\"/><Experiment acc=\"SRX20810435\" ver=\"2\" status=\"public\" name=\"GSM7518068: TSF1b, Lungs from TSF Injection, Metastatic Seeding (d11), Replicate b; Mus musculus; RNA-Seq\"/><Study acc=\"SRP446371\" name=\"Aspartate signaling increases the aggressiveness of lung metastases by inducing eIF5A-mediated translation (scRNA-Seq)\"/><Organism taxid=\"10090\" ScientificName=\"Mus musculus\"/><Sample acc=\"SRS18093900\" name=\"\"/><Instrument ILLUMINA=\"Illumina NovaSeq 6000\"/><Library_descriptor><LIBRARY_NAME>GSM7518068</LIBRARY_NAME><LIBRARY_STRATEGY>RNA-Seq</LIBRARY_STRATEGY><LIBRARY_SOURCE>TRANSCRIPTOMIC SINGLE CELL</LIBRARY_SOURCE><LIBRARY_SELECTION>cDNA</LIBRARY_SELECTION><LIBRARY_LAYOUT><PAIRED/></LIBRARY_LAYOUT><LIBRARY_CONSTRUCTION_PROTOCOL>Upon mice euthanasia, lungs were extracted and washed in blood bank saline, dried, and minced for ~ 2 minutes using blades. Minced lung tissues were then incubated with Liberase (0.3 mg/mL) and DNAse1 (1 \u03bcg/mL) for 45 min at 37\u00b0C, with occasional vortexing. The reaction was then quenched with PBS + 3% FBS + 2mM EDTA, after which cells were filtered through a 70\u03bcm cell strainer, washed once, and incubated with Red Blood Cell Lysis buffer. After red blood cell lysis, cells were washed once more and transferred through a 40 \u03bcm cell strainer. Cells were then pooled together from the 3 independent lung dissociations performed per group, resuspended in cell-culture medium at a density of 10^6 cells/mL, and kept on ice for immediate processing into single-cell cDNA libraries. Cell suspensions for each sample were converted to barcoded single-cell cDNA libraries using the Chromium Single Cell 5' v1.1 Library Kit, following the manufacturer's guidelines, and aiming for a total of 10,000 cells per library.</LIBRARY_CONSTRUCTION_PROTOCOL></Library_descriptor><Bioproject>PRJNA988806</Bioproject><Biosample>SAMN36028298</Biosample> ",
"runs": " <Run acc=\"SRR25056226\" total_spots=\"321922508\" total_bases=\"38308778452\" load_done=\"true\" is_public=\"true\" cluster_name=\"public\" static_data_available=\"true\"/> ",
"extlinks": "",
"createdate": "2024/10/04",
"updatedate": "2023/06/28"
},
"28241756": {
"uid": "28241756",
"expxml": " <Summary><Title>GSM7518067: TSF1a, Lungs from TSF Injection, Metastatic Seeding (d11), Replicate a; Mus musculus; RNA-Seq</Title><Platform instrument_model=\"Illumina NovaSeq 6000\">ILLUMINA</Platform><Statistics total_runs=\"1\" total_spots=\"362167958\" total_bases=\"43097987002\" total_size=\"14474390207\" load_done=\"true\" cluster_name=\"public\"/></Summary><Submitter acc=\"SRA1663813\" center_name=\"Laboratory of Cellular Metabolism and Metabolic Re\" contact_name=\"GEO Group\" lab_name=\"\"/><Experiment acc=\"SRX20810434\" ver=\"2\" status=\"public\" name=\"GSM7518067: TSF1a, Lungs from TSF Injection, Metastatic Seeding (d11), Replicate a; Mus musculus; RNA-Seq\"/><Study acc=\"SRP446371\" name=\"Aspartate signaling increases the aggressiveness of lung metastases by inducing eIF5A-mediated translation (scRNA-Seq)\"/><Organism taxid=\"10090\" ScientificName=\"Mus musculus\"/><Sample acc=\"SRS18093898\" name=\"\"/><Instrument ILLUMINA=\"Illumina NovaSeq 6000\"/><Library_descriptor><LIBRARY_NAME>GSM7518067</LIBRARY_NAME><LIBRARY_STRATEGY>RNA-Seq</LIBRARY_STRATEGY><LIBRARY_SOURCE>TRANSCRIPTOMIC SINGLE CELL</LIBRARY_SOURCE><LIBRARY_SELECTION>cDNA</LIBRARY_SELECTION><LIBRARY_LAYOUT><PAIRED/></LIBRARY_LAYOUT><LIBRARY_CONSTRUCTION_PROTOCOL>Upon mice euthanasia, lungs were extracted and washed in blood bank saline, dried, and minced for ~ 2 minutes using blades. Minced lung tissues were then incubated with Liberase (0.3 mg/mL) and DNAse1 (1 \u03bcg/mL) for 45 min at 37\u00b0C, with occasional vortexing. The reaction was then quenched with PBS + 3% FBS + 2mM EDTA, after which cells were filtered through a 70\u03bcm cell strainer, washed once, and incubated with Red Blood Cell Lysis buffer. After red blood cell lysis, cells were washed once more and transferred through a 40 \u03bcm cell strainer. Cells were then pooled together from the 3 independent lung dissociations performed per group, resuspended in cell-culture medium at a density of 10^6 cells/mL, and kept on ice for immediate processing into single-cell cDNA libraries. Cell suspensions for each sample were converted to barcoded single-cell cDNA libraries using the Chromium Single Cell 5' v1.1 Library Kit, following the manufacturer's guidelines, and aiming for a total of 10,000 cells per library.</LIBRARY_CONSTRUCTION_PROTOCOL></Library_descriptor><Bioproject>PRJNA988806</Bioproject><Biosample>SAMN36028299</Biosample> ",
"runs": " <Run acc=\"SRR25056227\" total_spots=\"362167958\" total_bases=\"43097987002\" load_done=\"true\" is_public=\"true\" cluster_name=\"public\" static_data_available=\"true\"/> ",
"extlinks": "",
"createdate": "2024/10/04",
"updatedate": "2023/06/28"
},
"28241755": {
"uid": "28241755",
"expxml": " <Summary><Title>GSM7518066: CM2, Lungs from CM Injection, Metastatic Colonization (d16); Mus musculus; RNA-Seq</Title><Platform instrument_model=\"Illumina NovaSeq 6000\">ILLUMINA</Platform><Statistics total_runs=\"1\" total_spots=\"339308480\" total_bases=\"40377709120\" total_size=\"13796528558\" load_done=\"true\" cluster_name=\"public\"/></Summary><Submitter acc=\"SRA1663813\" center_name=\"Laboratory of Cellular Metabolism and Metabolic Re\" contact_name=\"GEO Group\" lab_name=\"\"/><Experiment acc=\"SRX20810433\" ver=\"2\" status=\"public\" name=\"GSM7518066: CM2, Lungs from CM Injection, Metastatic Colonization (d16); Mus musculus; RNA-Seq\"/><Study acc=\"SRP446371\" name=\"Aspartate signaling increases the aggressiveness of lung metastases by inducing eIF5A-mediated translation (scRNA-Seq)\"/><Organism taxid=\"10090\" ScientificName=\"Mus musculus\"/><Sample acc=\"SRS18093897\" name=\"\"/><Instrument ILLUMINA=\"Illumina NovaSeq 6000\"/><Library_descriptor><LIBRARY_NAME>GSM7518066</LIBRARY_NAME><LIBRARY_STRATEGY>RNA-Seq</LIBRARY_STRATEGY><LIBRARY_SOURCE>TRANSCRIPTOMIC SINGLE CELL</LIBRARY_SOURCE><LIBRARY_SELECTION>cDNA</LIBRARY_SELECTION><LIBRARY_LAYOUT><PAIRED/></LIBRARY_LAYOUT><LIBRARY_CONSTRUCTION_PROTOCOL>Upon mice euthanasia, lungs were extracted and washed in blood bank saline, dried, and minced for ~ 2 minutes using blades. Minced lung tissues were then incubated with Liberase (0.3 mg/mL) and DNAse1 (1 \u03bcg/mL) for 45 min at 37\u00b0C, with occasional vortexing. The reaction was then quenched with PBS + 3% FBS + 2mM EDTA, after which cells were filtered through a 70\u03bcm cell strainer, washed once, and incubated with Red Blood Cell Lysis buffer. After red blood cell lysis, cells were washed once more and transferred through a 40 \u03bcm cell strainer. Cells were then pooled together from the 3 independent lung dissociations performed per group, resuspended in cell-culture medium at a density of 10^6 cells/mL, and kept on ice for immediate processing into single-cell cDNA libraries. Cell suspensions for each sample were converted to barcoded single-cell cDNA libraries using the Chromium Single Cell 5' v1.1 Library Kit, following the manufacturer's guidelines, and aiming for a total of 10,000 cells per library.</LIBRARY_CONSTRUCTION_PROTOCOL></Library_descriptor><Bioproject>PRJNA988806</Bioproject><Biosample>SAMN36028300</Biosample> ",
"runs": " <Run acc=\"SRR25056228\" total_spots=\"339308480\" total_bases=\"40377709120\" load_done=\"true\" is_public=\"true\" cluster_name=\"public\" static_data_available=\"true\"/> ",
"extlinks": "",
"createdate": "2024/10/04",
"updatedate": "2023/06/28"
},
"28241754": {
"uid": "28241754",
"expxml": " <Summary><Title>GSM7518065: CM1, Lungs from CM Injection, Metastatic Seeding (d11); Mus musculus; RNA-Seq</Title><Platform instrument_model=\"Illumina NovaSeq 6000\">ILLUMINA</Platform><Statistics total_runs=\"1\" total_spots=\"325016382\" total_bases=\"38676949458\" total_size=\"13072276347\" load_done=\"true\" cluster_name=\"public\"/></Summary><Submitter acc=\"SRA1663813\" center_name=\"Laboratory of Cellular Metabolism and Metabolic Re\" contact_name=\"GEO Group\" lab_name=\"\"/><Experiment acc=\"SRX20810432\" ver=\"2\" status=\"public\" name=\"GSM7518065: CM1, Lungs from CM Injection, Metastatic Seeding (d11); Mus musculus; RNA-Seq\"/><Study acc=\"SRP446371\" name=\"Aspartate signaling increases the aggressiveness of lung metastases by inducing eIF5A-mediated translation (scRNA-Seq)\"/><Organism taxid=\"10090\" ScientificName=\"Mus musculus\"/><Sample acc=\"SRS18093896\" name=\"\"/><Instrument ILLUMINA=\"Illumina NovaSeq 6000\"/><Library_descriptor><LIBRARY_NAME>GSM7518065</LIBRARY_NAME><LIBRARY_STRATEGY>RNA-Seq</LIBRARY_STRATEGY><LIBRARY_SOURCE>TRANSCRIPTOMIC SINGLE CELL</LIBRARY_SOURCE><LIBRARY_SELECTION>cDNA</LIBRARY_SELECTION><LIBRARY_LAYOUT><PAIRED/></LIBRARY_LAYOUT><LIBRARY_CONSTRUCTION_PROTOCOL>Upon mice euthanasia, lungs were extracted and washed in blood bank saline, dried, and minced for ~ 2 minutes using blades. Minced lung tissues were then incubated with Liberase (0.3 mg/mL) and DNAse1 (1 \u03bcg/mL) for 45 min at 37\u00b0C, with occasional vortexing. The reaction was then quenched with PBS + 3% FBS + 2mM EDTA, after which cells were filtered through a 70\u03bcm cell strainer, washed once, and incubated with Red Blood Cell Lysis buffer. After red blood cell lysis, cells were washed once more and transferred through a 40 \u03bcm cell strainer. Cells were then pooled together from the 3 independent lung dissociations performed per group, resuspended in cell-culture medium at a density of 10^6 cells/mL, and kept on ice for immediate processing into single-cell cDNA libraries. Cell suspensions for each sample were converted to barcoded single-cell cDNA libraries using the Chromium Single Cell 5' v1.1 Library Kit, following the manufacturer's guidelines, and aiming for a total of 10,000 cells per library.</LIBRARY_CONSTRUCTION_PROTOCOL></Library_descriptor><Bioproject>PRJNA988806</Bioproject><Biosample>SAMN36028301</Biosample> ",
"runs": " <Run acc=\"SRR25056229\" total_spots=\"325016382\" total_bases=\"38676949458\" load_done=\"true\" is_public=\"true\" cluster_name=\"public\" static_data_available=\"true\"/> ",
"extlinks": "",
"createdate": "2024/10/04",
"updatedate": "2023/06/28"
}
}
}
Summary gives us a lot of information about the SRA experiments, including the experiment title, platform, library construction protocol, and most importantly the run accessions. But the problem is that the run accessions are buried in the expxml field, which is not very convenient to parse. We can try using fetch instead of summary to get the run accessions in a more structured format:
eutils_fetch(
db="sra",
webenv=search_results["esearchresult"]["webenv"],
query_key=search_results["esearchresult"]["querykey"],
api_key=NCBI_API_KEY,
rettype="runinfo",
retmode="text",
)
Run,ReleaseDate,LoadDate,spots,bases,spots_with_mates,avgLength,size_MB,AssemblyName,download_path,Experiment,LibraryName,LibraryStrategy,LibrarySelection,LibrarySource,LibraryLayout,InsertSize,InsertDev,Platform,Model,SRAStudy,BioProject,Study_Pubmed_id,ProjectID,Sample,BioSample,SampleType,TaxID,ScientificName,SampleName,g1k_pop_code,source,g1k_analysis_group,Subject_ID,Sex,Disease,Tumor,Affection_Status,Analyte_Type,Histological_Type,Body_Site,CenterName,Submission,dbgap_study_accession,Consent,RunHash,ReadHash
SRR25056229,2024-10-04 14:39:07,2023-06-28 20:50:33,325016382,38676949458,325016382,119,12466,,https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos4/sra-pub-zq-7/SRR025/25056/SRR25056229/SRR25056229.lite.1,SRX20810432,GSM7518065,RNA-Seq,cDNA,TRANSCRIPTOMIC SINGLE CELL,PAIRED,0,0,ILLUMINA,Illumina NovaSeq 6000,SRP446371,PRJNA988806,3,988806,SRS18093896,SAMN36028301,simple,10090,Mus musculus,GSM7518065,,,,,,,no,,,,,"LABORATORY OF CELLULAR METABOLISM AND METABOLIC REGULATION, VIB-KU LEUVEN CENTER FOR CANCER BIOLOGY, VIB/KU LEUVEN",SRA1663699,,public,12A0013D89E3EA09D732E909D80A4EA0,16565C220BB5BF8C76B09379099F5662
SRR25056228,2024-10-04 14:39:07,2023-06-28 20:52:00,339308480,40377709120,339308480,119,13157,,https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos4/sra-pub-zq-7/SRR025/25056/SRR25056228/SRR25056228.lite.1,SRX20810433,GSM7518066,RNA-Seq,cDNA,TRANSCRIPTOMIC SINGLE CELL,PAIRED,0,0,ILLUMINA,Illumina NovaSeq 6000,SRP446371,PRJNA988806,3,988806,SRS18093897,SAMN36028300,simple,10090,Mus musculus,GSM7518066,,,,,,,no,,,,,"LABORATORY OF CELLULAR METABOLISM AND METABOLIC REGULATION, VIB-KU LEUVEN CENTER FOR CANCER BIOLOGY, VIB/KU LEUVEN",SRA1663699,,public,EF36BDA7FDE7BCB3B903A1CA26F62A1B,81566D41964391F8570324D21223A27A
SRR25056227,2024-10-04 14:39:07,2023-06-28 21:20:29,362167958,43097987002,362167958,119,13803,,https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos4/sra-pub-zq-7/SRR025/25056/SRR25056227/SRR25056227.lite.1,SRX20810434,GSM7518067,RNA-Seq,cDNA,TRANSCRIPTOMIC SINGLE CELL,PAIRED,0,0,ILLUMINA,Illumina NovaSeq 6000,SRP446371,PRJNA988806,3,988806,SRS18093898,SAMN36028299,simple,10090,Mus musculus,GSM7518067,,,,,,,no,,,,,"LABORATORY OF CELLULAR METABOLISM AND METABOLIC REGULATION, VIB-KU LEUVEN CENTER FOR CANCER BIOLOGY, VIB/KU LEUVEN",SRA1663699,,public,6671EE3C3CDAEE4DED10C126D99F2866,1C19A18F04FAC05BCFC819827271AB51
SRR25056226,2024-10-04 14:39:08,2023-06-28 21:26:02,321922508,38308778452,321922508,119,12382,,https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos4/sra-pub-zq-7/SRR025/25056/SRR25056226/SRR25056226.lite.1,SRX20810435,GSM7518068,RNA-Seq,cDNA,TRANSCRIPTOMIC SINGLE CELL,PAIRED,0,0,ILLUMINA,Illumina NovaSeq 6000,SRP446371,PRJNA988806,3,988806,SRS18093900,SAMN36028298,simple,10090,Mus musculus,GSM7518068,,,,,,,no,,,,,"LABORATORY OF CELLULAR METABOLISM AND METABOLIC REGULATION, VIB-KU LEUVEN CENTER FOR CANCER BIOLOGY, VIB/KU LEUVEN",SRA1663699,,public,31E9A4D84C4AFA2EAF45F87434E3FF59,1F37CFEF2DD30C50C859D5B0B39E485B
SRR25056225,2024-10-04 14:39:08,2023-06-28 21:08:06,332639939,39584152741,332639939,119,12714,,https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos4/sra-pub-zq-7/SRR025/25056/SRR25056225/SRR25056225.lite.1,SRX20810436,GSM7518069,RNA-Seq,cDNA,TRANSCRIPTOMIC SINGLE CELL,PAIRED,0,0,ILLUMINA,Illumina NovaSeq 6000,SRP446371,PRJNA988806,3,988806,SRS18093899,SAMN36028297,simple,10090,Mus musculus,GSM7518069,,,,,,,no,,,,,"LABORATORY OF CELLULAR METABOLISM AND METABOLIC REGULATION, VIB-KU LEUVEN CENTER FOR CANCER BIOLOGY, VIB/KU LEUVEN",SRA1663699,,public,07FB912346833E77F21C3F0D0C3B8935,C6ECC1BDE321FD04338FFC225F6EBF73
We can also get csv output using sra-db-be API, which is more efficient for fetching large number of records and which sometimes contains more up-to-date information than the eutils API:
base = "https://trace.ncbi.nlm.nih.gov/Traces/sra-db-be/sra-"
params = {
"WebEnv": search_results["esearchresult"]["webenv"],
"rettype": "runinfo",
"query_key": search_results["esearchresult"]["querykey"],
}
response = httpx.get(base, params=params)
response.raise_for_status()
print(response.text)
Run,ReleaseDate,LoadDate,spots,bases,spots_with_mates,avgLength,size_MB,AssemblyName,download_path,Experiment,LibraryName,LibraryStrategy,LibrarySelection,LibrarySource,LibraryLayout,InsertSize,InsertDev,Platform,Model,SRAStudy,BioProject,Study_Pubmed_id,ProjectID,Sample,BioSample,SampleType,TaxID,ScientificName,SampleName,g1k_pop_code,source,g1k_analysis_group,Subject_ID,Sex,Disease,Tumor,Affection_Status,Analyte_Type,Histological_Type,Body_Site,CenterName,Submission,dbgap_study_accession,Consent,RunHash,ReadHash
SRR25056229,2024-10-04 14:39:07,2023-06-28 20:50:33,325016382,38676949458,325016382,119,12466,,https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos4/sra-pub-zq-7/SRR025/25056/SRR25056229/SRR25056229.lite.1,SRX20810432,GSM7518065,RNA-Seq,cDNA,TRANSCRIPTOMIC SINGLE CELL,PAIRED,0,0,ILLUMINA,Illumina NovaSeq 6000,SRP446371,PRJNA988806,3,988806,SRS18093896,SAMN36028301,simple,10090,Mus musculus,GSM7518065,,,,,,,no,,,,,"LABORATORY OF CELLULAR METABOLISM AND METABOLIC REGULATION, VIB-KU LEUVEN CENTER FOR CANCER BIOLOGY, VIB/KU LEUVEN",SRA1663699,,public,12A0013D89E3EA09D732E909D80A4EA0,16565C220BB5BF8C76B09379099F5662
SRR25056228,2024-10-04 14:39:07,2023-06-28 20:52:00,339308480,40377709120,339308480,119,13157,,https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos4/sra-pub-zq-7/SRR025/25056/SRR25056228/SRR25056228.lite.1,SRX20810433,GSM7518066,RNA-Seq,cDNA,TRANSCRIPTOMIC SINGLE CELL,PAIRED,0,0,ILLUMINA,Illumina NovaSeq 6000,SRP446371,PRJNA988806,3,988806,SRS18093897,SAMN36028300,simple,10090,Mus musculus,GSM7518066,,,,,,,no,,,,,"LABORATORY OF CELLULAR METABOLISM AND METABOLIC REGULATION, VIB-KU LEUVEN CENTER FOR CANCER BIOLOGY, VIB/KU LEUVEN",SRA1663699,,public,EF36BDA7FDE7BCB3B903A1CA26F62A1B,81566D41964391F8570324D21223A27A
SRR25056227,2024-10-04 14:39:07,2023-06-28 21:20:29,362167958,43097987002,362167958,119,13803,,https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos4/sra-pub-zq-7/SRR025/25056/SRR25056227/SRR25056227.lite.1,SRX20810434,GSM7518067,RNA-Seq,cDNA,TRANSCRIPTOMIC SINGLE CELL,PAIRED,0,0,ILLUMINA,Illumina NovaSeq 6000,SRP446371,PRJNA988806,3,988806,SRS18093898,SAMN36028299,simple,10090,Mus musculus,GSM7518067,,,,,,,no,,,,,"LABORATORY OF CELLULAR METABOLISM AND METABOLIC REGULATION, VIB-KU LEUVEN CENTER FOR CANCER BIOLOGY, VIB/KU LEUVEN",SRA1663699,,public,6671EE3C3CDAEE4DED10C126D99F2866,1C19A18F04FAC05BCFC819827271AB51
SRR25056226,2024-10-04 14:39:08,2023-06-28 21:26:02,321922508,38308778452,321922508,119,12382,,https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos4/sra-pub-zq-7/SRR025/25056/SRR25056226/SRR25056226.lite.1,SRX20810435,GSM7518068,RNA-Seq,cDNA,TRANSCRIPTOMIC SINGLE CELL,PAIRED,0,0,ILLUMINA,Illumina NovaSeq 6000,SRP446371,PRJNA988806,3,988806,SRS18093900,SAMN36028298,simple,10090,Mus musculus,GSM7518068,,,,,,,no,,,,,"LABORATORY OF CELLULAR METABOLISM AND METABOLIC REGULATION, VIB-KU LEUVEN CENTER FOR CANCER BIOLOGY, VIB/KU LEUVEN",SRA1663699,,public,31E9A4D84C4AFA2EAF45F87434E3FF59,1F37CFEF2DD30C50C859D5B0B39E485B
SRR25056225,2024-10-04 14:39:08,2023-06-28 21:08:06,332639939,39584152741,332639939,119,12714,,https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos4/sra-pub-zq-7/SRR025/25056/SRR25056225/SRR25056225.lite.1,SRX20810436,GSM7518069,RNA-Seq,cDNA,TRANSCRIPTOMIC SINGLE CELL,PAIRED,0,0,ILLUMINA,Illumina NovaSeq 6000,SRP446371,PRJNA988806,3,988806,SRS18093899,SAMN36028297,simple,10090,Mus musculus,GSM7518069,,,,,,,no,,,,,"LABORATORY OF CELLULAR METABOLISM AND METABOLIC REGULATION, VIB-KU LEUVEN CENTER FOR CANCER BIOLOGY, VIB/KU LEUVEN",SRA1663699,,public,07FB912346833E77F21C3F0D0C3B8935,C6ECC1BDE321FD04338FFC225F6EBF73
Good, we have successfully fetched the SRA experiments linked to this BioProject. We can see that there are 5 experiments, each corresponding to a different sample that was sequenced in the study. Each experiment contains information about the library construction protocol, the instrument used for sequencing, the number of runs, spots, bases and size of the data, as well as links to the corresponding BioSample and BioProject records.
BioProject to ENA¶
Finally let's try to fetch ENA records linked to this BioProject using the second link:
fields = [
"study_accession",
"secondary_study_accession",
"sample_accession",
"sample_alias",
"secondary_sample_accession",
"experiment_accession",
"experiment_alias",
"run_accession",
"run_alias"
]
read_enaruns(
series="PRJNA988806",
format="json",
fields=",".join(fields),
)
[
{
"run_accession": "SRR25056226",
"study_accession": "PRJNA988806",
"secondary_study_accession": "SRP446371",
"sample_accession": "SAMN36028298",
"sample_alias": "GSM7518068",
"secondary_sample_accession": "SRS18093900",
"experiment_accession": "SRX20810435",
"experiment_alias": "GSM7518068_r1",
"run_alias": "GSM7518068_r1"
},
{
"run_accession": "SRR25056229",
"study_accession": "PRJNA988806",
"secondary_study_accession": "SRP446371",
"sample_accession": "SAMN36028301",
"sample_alias": "GSM7518065",
"secondary_sample_accession": "SRS18093896",
"experiment_accession": "SRX20810432",
"experiment_alias": "GSM7518065_r1",
"run_alias": "GSM7518065_r1"
},
{
"run_accession": "SRR25056227",
"study_accession": "PRJNA988806",
"secondary_study_accession": "SRP446371",
"sample_accession": "SAMN36028299",
"sample_alias": "GSM7518067",
"secondary_sample_accession": "SRS18093898",
"experiment_accession": "SRX20810434",
"experiment_alias": "GSM7518067_r1",
"run_alias": "GSM7518067_r1"
},
{
"run_accession": "SRR25056228",
"study_accession": "PRJNA988806",
"secondary_study_accession": "SRP446371",
"sample_accession": "SAMN36028300",
"sample_alias": "GSM7518066",
"secondary_sample_accession": "SRS18093897",
"experiment_accession": "SRX20810433",
"experiment_alias": "GSM7518066_r1",
"run_alias": "GSM7518066_r1"
},
{
"run_accession": "SRR25056225",
"study_accession": "PRJNA988806",
"secondary_study_accession": "SRP446371",
"sample_accession": "SAMN36028297",
"sample_alias": "GSM7518069",
"secondary_sample_accession": "SRS18093899",
"experiment_accession": "SRX20810436",
"experiment_alias": "GSM7518069_r1",
"run_alias": "GSM7518069_r1"
}
]
Following Links¶
We will reuse the search result for BioProject PRJNA988806 to follow links to other databases. We will start with GEO, then SRA and finally ENA.
BioProject to GEO¶
Let's start with GEO datasets linked to this BioProject.
eutils_link(
dbfrom="bioproject",
db="gds",
webenv=search_results["esearchresult"]["webenv"],
query_key=search_results["esearchresult"]["querykey"],
)
{
"header": {
"type": "elink",
"version": "0.3"
},
"linksets": [
{
"dbfrom": "bioproject",
"ids": [
"988806"
],
"linksetdbhistories": [
{
"dbto": "gds",
"linkname": "bioproject_gds",
"querykey": "2"
}
],
"webenv": "MCID_69f379d2a5849e8d8c0781b5"
}
]
}
We can see that there is a link to the GEO DataSet database, with a query key of 2. We can use this query key to fetch the linked GEO datasets:
eutils_summary(
webenv=links["linksets"][0]["webenv"],
query_key=links["linksets"][0]["linksetdbhistories"][0]["querykey"],
db="gds",
)
{
"header": {
"type": "esummary",
"version": "0.3"
},
"result": {
"uids": [
"200236084"
],
"200236084": {
"uid": "200236084",
"accession": "GSE236084",
"gds": "",
"title": "Aspartate signaling increases the aggressiveness of lung metastases by inducing eIF5A-mediated translation (scRNA-Seq)",
"summary": "Lung metastases are detected in more than half of patients with metastatic tumors. However, it remains largely unknown why the lung environment is a permissive niche for metastases. Here, we discover that pulmonary aspartate triggers a cellular signaling cascade in disseminated cancer cells resulting in a translational program that boosts lung metastasis. Specifically, we observe that patients and mice with breast cancer have high concentrations of aspartate in their lung interstitial fluid. This extracellular aspartate activates the ionotropic N-methyl-D-aspartate (NMDA) receptor in cancer cells, which induces CREB-dependent mRNA expression of deoxyhypusine hydroxylase (DOHH). The latter is essential for hypusination, a posttranslational modification required for the activity of the non-classical translation initiation factor eIF5A. In turn, a translational program with TGF-\u03b2 signaling as a central hub promotes collagen remodeling in the disseminated breast cancer cells. We detect key aspects of this mechanism in lung metastases from patients with breast cancer. In summary, we discover that pulmonary aspartate increases with breast cancer and induces a signaling cascade promoting the growth of lung metastases.",
"gpl": "24247",
"gse": "236084",
"taxon": "Mus musculus",
"entrytype": "GSE",
"gdstype": "Expression profiling by high throughput sequencing",
"ptechtype": "",
"valtype": "",
"ssinfo": "",
"subsetinfo": "",
"pdat": "2024/10/04",
"suppfile": "TAR, TXT",
"samples": [
{
"accession": "GSM7518067",
"title": "TSF1a, Lungs from TSF Injection, Metastatic Seeding (d11), Replicate a"
},
{
"accession": "GSM7518065",
"title": "CM1, Lungs from CM Injection, Metastatic Seeding (d11)"
},
{
"accession": "GSM7518068",
"title": "TSF1b, Lungs from TSF Injection, Metastatic Seeding (d11), Replicate b"
},
{
"accession": "GSM7518066",
"title": "CM2, Lungs from CM Injection, Metastatic Colonization (d16)"
},
{
"accession": "GSM7518069",
"title": "TSF2, Lungs from TSF Injection, Metastatic Colonization (d16)"
}
],
"relations": [],
"extrelations": [],
"n_samples": 5,
"seriestitle": "",
"platformtitle": "",
"platformtaxa": "",
"samplestaxa": "",
"pubmedids": [
"39743589"
],
"projects": [],
"ftplink": "ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE236nnn/GSE236084/",
"geo2r": "no",
"bioproject": "PRJNA988806"
}
}
}
BioProject to SRA¶
In the same way we can also fetch the linked SRA experiments for this BioProject, let's try that:
eutils_link(
dbfrom="bioproject",
db="sra",
webenv=search_results["esearchresult"]["webenv"],
query_key=search_results["esearchresult"]["querykey"],
)
{
"header": {
"type": "elink",
"version": "0.3"
},
"linksets": [
{
"dbfrom": "bioproject",
"ids": [
"988806"
],
"linksetdbhistories": [
{
"dbto": "sra",
"linkname": "bioproject_sra",
"querykey": "3"
},
{
"dbto": "sra",
"linkname": "bioproject_sra_all",
"querykey": "4"
}
],
"webenv": "MCID_69f379d2a5849e8d8c0781b5"
}
]
}
We can see that there are two links to the SRA database, one with the link name bioproject_sra and another with the link name bioproject_sra_all. The first one will give us the SRA experiments that are directly linked to the BioProject, while the second one will give us all the SRA experiments that are linked to the BioProject, including those that are linked through BioSamples. Let's fetch the SRA experiments using the first link:
eutils_summary(
webenv=links["linksets"][0]["webenv"],
query_key=links["linksets"][0]["linksetdbhistories"][0]["querykey"],
db="sra",
)
{
"header": {
"type": "esummary",
"version": "0.3"
},
"result": {
"uids": [
"28241758",
"28241757",
"28241756",
"28241755",
"28241754"
],
"28241758": {
"uid": "28241758",
"expxml": " <Summary><Title>GSM7518069: TSF2, Lungs from TSF Injection, Metastatic Colonization (d16); Mus musculus; RNA-Seq</Title><Platform instrument_model=\"Illumina NovaSeq 6000\">ILLUMINA</Platform><Statistics total_runs=\"1\" total_spots=\"332639939\" total_bases=\"39584152741\" total_size=\"13332204657\" load_done=\"true\" cluster_name=\"public\"/></Summary><Submitter acc=\"SRA1663813\" center_name=\"Laboratory of Cellular Metabolism and Metabolic Re\" contact_name=\"GEO Group\" lab_name=\"\"/><Experiment acc=\"SRX20810436\" ver=\"2\" status=\"public\" name=\"GSM7518069: TSF2, Lungs from TSF Injection, Metastatic Colonization (d16); Mus musculus; RNA-Seq\"/><Study acc=\"SRP446371\" name=\"Aspartate signaling increases the aggressiveness of lung metastases by inducing eIF5A-mediated translation (scRNA-Seq)\"/><Organism taxid=\"10090\" ScientificName=\"Mus musculus\"/><Sample acc=\"SRS18093899\" name=\"\"/><Instrument ILLUMINA=\"Illumina NovaSeq 6000\"/><Library_descriptor><LIBRARY_NAME>GSM7518069</LIBRARY_NAME><LIBRARY_STRATEGY>RNA-Seq</LIBRARY_STRATEGY><LIBRARY_SOURCE>TRANSCRIPTOMIC SINGLE CELL</LIBRARY_SOURCE><LIBRARY_SELECTION>cDNA</LIBRARY_SELECTION><LIBRARY_LAYOUT><PAIRED/></LIBRARY_LAYOUT><LIBRARY_CONSTRUCTION_PROTOCOL>Upon mice euthanasia, lungs were extracted and washed in blood bank saline, dried, and minced for ~ 2 minutes using blades. Minced lung tissues were then incubated with Liberase (0.3 mg/mL) and DNAse1 (1 \u03bcg/mL) for 45 min at 37\u00b0C, with occasional vortexing. The reaction was then quenched with PBS + 3% FBS + 2mM EDTA, after which cells were filtered through a 70\u03bcm cell strainer, washed once, and incubated with Red Blood Cell Lysis buffer. After red blood cell lysis, cells were washed once more and transferred through a 40 \u03bcm cell strainer. Cells were then pooled together from the 3 independent lung dissociations performed per group, resuspended in cell-culture medium at a density of 10^6 cells/mL, and kept on ice for immediate processing into single-cell cDNA libraries. Cell suspensions for each sample were converted to barcoded single-cell cDNA libraries using the Chromium Single Cell 5' v1.1 Library Kit, following the manufacturer's guidelines, and aiming for a total of 10,000 cells per library.</LIBRARY_CONSTRUCTION_PROTOCOL></Library_descriptor><Bioproject>PRJNA988806</Bioproject><Biosample>SAMN36028297</Biosample> ",
"runs": " <Run acc=\"SRR25056225\" total_spots=\"332639939\" total_bases=\"39584152741\" load_done=\"true\" is_public=\"true\" cluster_name=\"public\" static_data_available=\"true\"/> ",
"extlinks": "",
"createdate": "2024/10/04",
"updatedate": "2023/06/28"
},
"28241757": {
"uid": "28241757",
"expxml": " <Summary><Title>GSM7518068: TSF1b, Lungs from TSF Injection, Metastatic Seeding (d11), Replicate b; Mus musculus; RNA-Seq</Title><Platform instrument_model=\"Illumina NovaSeq 6000\">ILLUMINA</Platform><Statistics total_runs=\"1\" total_spots=\"321922508\" total_bases=\"38308778452\" total_size=\"12983749287\" load_done=\"true\" cluster_name=\"public\"/></Summary><Submitter acc=\"SRA1663813\" center_name=\"Laboratory of Cellular Metabolism and Metabolic Re\" contact_name=\"GEO Group\" lab_name=\"\"/><Experiment acc=\"SRX20810435\" ver=\"2\" status=\"public\" name=\"GSM7518068: TSF1b, Lungs from TSF Injection, Metastatic Seeding (d11), Replicate b; Mus musculus; RNA-Seq\"/><Study acc=\"SRP446371\" name=\"Aspartate signaling increases the aggressiveness of lung metastases by inducing eIF5A-mediated translation (scRNA-Seq)\"/><Organism taxid=\"10090\" ScientificName=\"Mus musculus\"/><Sample acc=\"SRS18093900\" name=\"\"/><Instrument ILLUMINA=\"Illumina NovaSeq 6000\"/><Library_descriptor><LIBRARY_NAME>GSM7518068</LIBRARY_NAME><LIBRARY_STRATEGY>RNA-Seq</LIBRARY_STRATEGY><LIBRARY_SOURCE>TRANSCRIPTOMIC SINGLE CELL</LIBRARY_SOURCE><LIBRARY_SELECTION>cDNA</LIBRARY_SELECTION><LIBRARY_LAYOUT><PAIRED/></LIBRARY_LAYOUT><LIBRARY_CONSTRUCTION_PROTOCOL>Upon mice euthanasia, lungs were extracted and washed in blood bank saline, dried, and minced for ~ 2 minutes using blades. Minced lung tissues were then incubated with Liberase (0.3 mg/mL) and DNAse1 (1 \u03bcg/mL) for 45 min at 37\u00b0C, with occasional vortexing. The reaction was then quenched with PBS + 3% FBS + 2mM EDTA, after which cells were filtered through a 70\u03bcm cell strainer, washed once, and incubated with Red Blood Cell Lysis buffer. After red blood cell lysis, cells were washed once more and transferred through a 40 \u03bcm cell strainer. Cells were then pooled together from the 3 independent lung dissociations performed per group, resuspended in cell-culture medium at a density of 10^6 cells/mL, and kept on ice for immediate processing into single-cell cDNA libraries. Cell suspensions for each sample were converted to barcoded single-cell cDNA libraries using the Chromium Single Cell 5' v1.1 Library Kit, following the manufacturer's guidelines, and aiming for a total of 10,000 cells per library.</LIBRARY_CONSTRUCTION_PROTOCOL></Library_descriptor><Bioproject>PRJNA988806</Bioproject><Biosample>SAMN36028298</Biosample> ",
"runs": " <Run acc=\"SRR25056226\" total_spots=\"321922508\" total_bases=\"38308778452\" load_done=\"true\" is_public=\"true\" cluster_name=\"public\" static_data_available=\"true\"/> ",
"extlinks": "",
"createdate": "2024/10/04",
"updatedate": "2023/06/28"
},
"28241756": {
"uid": "28241756",
"expxml": " <Summary><Title>GSM7518067: TSF1a, Lungs from TSF Injection, Metastatic Seeding (d11), Replicate a; Mus musculus; RNA-Seq</Title><Platform instrument_model=\"Illumina NovaSeq 6000\">ILLUMINA</Platform><Statistics total_runs=\"1\" total_spots=\"362167958\" total_bases=\"43097987002\" total_size=\"14474390207\" load_done=\"true\" cluster_name=\"public\"/></Summary><Submitter acc=\"SRA1663813\" center_name=\"Laboratory of Cellular Metabolism and Metabolic Re\" contact_name=\"GEO Group\" lab_name=\"\"/><Experiment acc=\"SRX20810434\" ver=\"2\" status=\"public\" name=\"GSM7518067: TSF1a, Lungs from TSF Injection, Metastatic Seeding (d11), Replicate a; Mus musculus; RNA-Seq\"/><Study acc=\"SRP446371\" name=\"Aspartate signaling increases the aggressiveness of lung metastases by inducing eIF5A-mediated translation (scRNA-Seq)\"/><Organism taxid=\"10090\" ScientificName=\"Mus musculus\"/><Sample acc=\"SRS18093898\" name=\"\"/><Instrument ILLUMINA=\"Illumina NovaSeq 6000\"/><Library_descriptor><LIBRARY_NAME>GSM7518067</LIBRARY_NAME><LIBRARY_STRATEGY>RNA-Seq</LIBRARY_STRATEGY><LIBRARY_SOURCE>TRANSCRIPTOMIC SINGLE CELL</LIBRARY_SOURCE><LIBRARY_SELECTION>cDNA</LIBRARY_SELECTION><LIBRARY_LAYOUT><PAIRED/></LIBRARY_LAYOUT><LIBRARY_CONSTRUCTION_PROTOCOL>Upon mice euthanasia, lungs were extracted and washed in blood bank saline, dried, and minced for ~ 2 minutes using blades. Minced lung tissues were then incubated with Liberase (0.3 mg/mL) and DNAse1 (1 \u03bcg/mL) for 45 min at 37\u00b0C, with occasional vortexing. The reaction was then quenched with PBS + 3% FBS + 2mM EDTA, after which cells were filtered through a 70\u03bcm cell strainer, washed once, and incubated with Red Blood Cell Lysis buffer. After red blood cell lysis, cells were washed once more and transferred through a 40 \u03bcm cell strainer. Cells were then pooled together from the 3 independent lung dissociations performed per group, resuspended in cell-culture medium at a density of 10^6 cells/mL, and kept on ice for immediate processing into single-cell cDNA libraries. Cell suspensions for each sample were converted to barcoded single-cell cDNA libraries using the Chromium Single Cell 5' v1.1 Library Kit, following the manufacturer's guidelines, and aiming for a total of 10,000 cells per library.</LIBRARY_CONSTRUCTION_PROTOCOL></Library_descriptor><Bioproject>PRJNA988806</Bioproject><Biosample>SAMN36028299</Biosample> ",
"runs": " <Run acc=\"SRR25056227\" total_spots=\"362167958\" total_bases=\"43097987002\" load_done=\"true\" is_public=\"true\" cluster_name=\"public\" static_data_available=\"true\"/> ",
"extlinks": "",
"createdate": "2024/10/04",
"updatedate": "2023/06/28"
},
"28241755": {
"uid": "28241755",
"expxml": " <Summary><Title>GSM7518066: CM2, Lungs from CM Injection, Metastatic Colonization (d16); Mus musculus; RNA-Seq</Title><Platform instrument_model=\"Illumina NovaSeq 6000\">ILLUMINA</Platform><Statistics total_runs=\"1\" total_spots=\"339308480\" total_bases=\"40377709120\" total_size=\"13796528558\" load_done=\"true\" cluster_name=\"public\"/></Summary><Submitter acc=\"SRA1663813\" center_name=\"Laboratory of Cellular Metabolism and Metabolic Re\" contact_name=\"GEO Group\" lab_name=\"\"/><Experiment acc=\"SRX20810433\" ver=\"2\" status=\"public\" name=\"GSM7518066: CM2, Lungs from CM Injection, Metastatic Colonization (d16); Mus musculus; RNA-Seq\"/><Study acc=\"SRP446371\" name=\"Aspartate signaling increases the aggressiveness of lung metastases by inducing eIF5A-mediated translation (scRNA-Seq)\"/><Organism taxid=\"10090\" ScientificName=\"Mus musculus\"/><Sample acc=\"SRS18093897\" name=\"\"/><Instrument ILLUMINA=\"Illumina NovaSeq 6000\"/><Library_descriptor><LIBRARY_NAME>GSM7518066</LIBRARY_NAME><LIBRARY_STRATEGY>RNA-Seq</LIBRARY_STRATEGY><LIBRARY_SOURCE>TRANSCRIPTOMIC SINGLE CELL</LIBRARY_SOURCE><LIBRARY_SELECTION>cDNA</LIBRARY_SELECTION><LIBRARY_LAYOUT><PAIRED/></LIBRARY_LAYOUT><LIBRARY_CONSTRUCTION_PROTOCOL>Upon mice euthanasia, lungs were extracted and washed in blood bank saline, dried, and minced for ~ 2 minutes using blades. Minced lung tissues were then incubated with Liberase (0.3 mg/mL) and DNAse1 (1 \u03bcg/mL) for 45 min at 37\u00b0C, with occasional vortexing. The reaction was then quenched with PBS + 3% FBS + 2mM EDTA, after which cells were filtered through a 70\u03bcm cell strainer, washed once, and incubated with Red Blood Cell Lysis buffer. After red blood cell lysis, cells were washed once more and transferred through a 40 \u03bcm cell strainer. Cells were then pooled together from the 3 independent lung dissociations performed per group, resuspended in cell-culture medium at a density of 10^6 cells/mL, and kept on ice for immediate processing into single-cell cDNA libraries. Cell suspensions for each sample were converted to barcoded single-cell cDNA libraries using the Chromium Single Cell 5' v1.1 Library Kit, following the manufacturer's guidelines, and aiming for a total of 10,000 cells per library.</LIBRARY_CONSTRUCTION_PROTOCOL></Library_descriptor><Bioproject>PRJNA988806</Bioproject><Biosample>SAMN36028300</Biosample> ",
"runs": " <Run acc=\"SRR25056228\" total_spots=\"339308480\" total_bases=\"40377709120\" load_done=\"true\" is_public=\"true\" cluster_name=\"public\" static_data_available=\"true\"/> ",
"extlinks": "",
"createdate": "2024/10/04",
"updatedate": "2023/06/28"
},
"28241754": {
"uid": "28241754",
"expxml": " <Summary><Title>GSM7518065: CM1, Lungs from CM Injection, Metastatic Seeding (d11); Mus musculus; RNA-Seq</Title><Platform instrument_model=\"Illumina NovaSeq 6000\">ILLUMINA</Platform><Statistics total_runs=\"1\" total_spots=\"325016382\" total_bases=\"38676949458\" total_size=\"13072276347\" load_done=\"true\" cluster_name=\"public\"/></Summary><Submitter acc=\"SRA1663813\" center_name=\"Laboratory of Cellular Metabolism and Metabolic Re\" contact_name=\"GEO Group\" lab_name=\"\"/><Experiment acc=\"SRX20810432\" ver=\"2\" status=\"public\" name=\"GSM7518065: CM1, Lungs from CM Injection, Metastatic Seeding (d11); Mus musculus; RNA-Seq\"/><Study acc=\"SRP446371\" name=\"Aspartate signaling increases the aggressiveness of lung metastases by inducing eIF5A-mediated translation (scRNA-Seq)\"/><Organism taxid=\"10090\" ScientificName=\"Mus musculus\"/><Sample acc=\"SRS18093896\" name=\"\"/><Instrument ILLUMINA=\"Illumina NovaSeq 6000\"/><Library_descriptor><LIBRARY_NAME>GSM7518065</LIBRARY_NAME><LIBRARY_STRATEGY>RNA-Seq</LIBRARY_STRATEGY><LIBRARY_SOURCE>TRANSCRIPTOMIC SINGLE CELL</LIBRARY_SOURCE><LIBRARY_SELECTION>cDNA</LIBRARY_SELECTION><LIBRARY_LAYOUT><PAIRED/></LIBRARY_LAYOUT><LIBRARY_CONSTRUCTION_PROTOCOL>Upon mice euthanasia, lungs were extracted and washed in blood bank saline, dried, and minced for ~ 2 minutes using blades. Minced lung tissues were then incubated with Liberase (0.3 mg/mL) and DNAse1 (1 \u03bcg/mL) for 45 min at 37\u00b0C, with occasional vortexing. The reaction was then quenched with PBS + 3% FBS + 2mM EDTA, after which cells were filtered through a 70\u03bcm cell strainer, washed once, and incubated with Red Blood Cell Lysis buffer. After red blood cell lysis, cells were washed once more and transferred through a 40 \u03bcm cell strainer. Cells were then pooled together from the 3 independent lung dissociations performed per group, resuspended in cell-culture medium at a density of 10^6 cells/mL, and kept on ice for immediate processing into single-cell cDNA libraries. Cell suspensions for each sample were converted to barcoded single-cell cDNA libraries using the Chromium Single Cell 5' v1.1 Library Kit, following the manufacturer's guidelines, and aiming for a total of 10,000 cells per library.</LIBRARY_CONSTRUCTION_PROTOCOL></Library_descriptor><Bioproject>PRJNA988806</Bioproject><Biosample>SAMN36028301</Biosample> ",
"runs": " <Run acc=\"SRR25056229\" total_spots=\"325016382\" total_bases=\"38676949458\" load_done=\"true\" is_public=\"true\" cluster_name=\"public\" static_data_available=\"true\"/> ",
"extlinks": "",
"createdate": "2024/10/04",
"updatedate": "2023/06/28"
}
}
}
We can see that there are 5 SRA experiments linked to this BioProject, which correspond to the 5 samples that were sequenced in the study. Each experiment has a unique accession number (SRX20810432, SRX20810433, SRX20810434, SRX20810435, SRX20810436) and contains information about the library construction protocol, the instrument used for sequencing, the number of runs, spots, bases and size of the data, as well as links to the corresponding BioSample and BioProject records.
We can also try fetching the SRA experiments in the csv format
eutils_fetch(
db="sra",
webenv=links["linksets"][0]["webenv"],
query_key=links["linksets"][0]["linksetdbhistories"][1]["querykey"],
api_key=NCBI_API_KEY,
rettype="runinfo",
retmode="text",
)
Run,ReleaseDate,LoadDate,spots,bases,spots_with_mates,avgLength,size_MB,AssemblyName,download_path,Experiment,LibraryName,LibraryStrategy,LibrarySelection,LibrarySource,LibraryLayout,InsertSize,InsertDev,Platform,Model,SRAStudy,BioProject,Study_Pubmed_id,ProjectID,Sample,BioSample,SampleType,TaxID,ScientificName,SampleName,g1k_pop_code,source,g1k_analysis_group,Subject_ID,Sex,Disease,Tumor,Affection_Status,Analyte_Type,Histological_Type,Body_Site,CenterName,Submission,dbgap_study_accession,Consent,RunHash,ReadHash
SRR25056229,2024-10-04 14:39:07,2023-06-28 20:50:33,325016382,38676949458,325016382,119,12466,,https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos4/sra-pub-zq-7/SRR025/25056/SRR25056229/SRR25056229.lite.1,SRX20810432,GSM7518065,RNA-Seq,cDNA,TRANSCRIPTOMIC SINGLE CELL,PAIRED,0,0,ILLUMINA,Illumina NovaSeq 6000,SRP446371,PRJNA988806,3,988806,SRS18093896,SAMN36028301,simple,10090,Mus musculus,GSM7518065,,,,,,,no,,,,,"LABORATORY OF CELLULAR METABOLISM AND METABOLIC REGULATION, VIB-KU LEUVEN CENTER FOR CANCER BIOLOGY, VIB/KU LEUVEN",SRA1663699,,public,12A0013D89E3EA09D732E909D80A4EA0,16565C220BB5BF8C76B09379099F5662
SRR25056228,2024-10-04 14:39:07,2023-06-28 20:52:00,339308480,40377709120,339308480,119,13157,,https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos4/sra-pub-zq-7/SRR025/25056/SRR25056228/SRR25056228.lite.1,SRX20810433,GSM7518066,RNA-Seq,cDNA,TRANSCRIPTOMIC SINGLE CELL,PAIRED,0,0,ILLUMINA,Illumina NovaSeq 6000,SRP446371,PRJNA988806,3,988806,SRS18093897,SAMN36028300,simple,10090,Mus musculus,GSM7518066,,,,,,,no,,,,,"LABORATORY OF CELLULAR METABOLISM AND METABOLIC REGULATION, VIB-KU LEUVEN CENTER FOR CANCER BIOLOGY, VIB/KU LEUVEN",SRA1663699,,public,EF36BDA7FDE7BCB3B903A1CA26F62A1B,81566D41964391F8570324D21223A27A
SRR25056227,2024-10-04 14:39:07,2023-06-28 21:20:29,362167958,43097987002,362167958,119,13803,,https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos4/sra-pub-zq-7/SRR025/25056/SRR25056227/SRR25056227.lite.1,SRX20810434,GSM7518067,RNA-Seq,cDNA,TRANSCRIPTOMIC SINGLE CELL,PAIRED,0,0,ILLUMINA,Illumina NovaSeq 6000,SRP446371,PRJNA988806,3,988806,SRS18093898,SAMN36028299,simple,10090,Mus musculus,GSM7518067,,,,,,,no,,,,,"LABORATORY OF CELLULAR METABOLISM AND METABOLIC REGULATION, VIB-KU LEUVEN CENTER FOR CANCER BIOLOGY, VIB/KU LEUVEN",SRA1663699,,public,6671EE3C3CDAEE4DED10C126D99F2866,1C19A18F04FAC05BCFC819827271AB51
SRR25056226,2024-10-04 14:39:08,2023-06-28 21:26:02,321922508,38308778452,321922508,119,12382,,https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos4/sra-pub-zq-7/SRR025/25056/SRR25056226/SRR25056226.lite.1,SRX20810435,GSM7518068,RNA-Seq,cDNA,TRANSCRIPTOMIC SINGLE CELL,PAIRED,0,0,ILLUMINA,Illumina NovaSeq 6000,SRP446371,PRJNA988806,3,988806,SRS18093900,SAMN36028298,simple,10090,Mus musculus,GSM7518068,,,,,,,no,,,,,"LABORATORY OF CELLULAR METABOLISM AND METABOLIC REGULATION, VIB-KU LEUVEN CENTER FOR CANCER BIOLOGY, VIB/KU LEUVEN",SRA1663699,,public,31E9A4D84C4AFA2EAF45F87434E3FF59,1F37CFEF2DD30C50C859D5B0B39E485B
SRR25056225,2024-10-04 14:39:08,2023-06-28 21:08:06,332639939,39584152741,332639939,119,12714,,https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos4/sra-pub-zq-7/SRR025/25056/SRR25056225/SRR25056225.lite.1,SRX20810436,GSM7518069,RNA-Seq,cDNA,TRANSCRIPTOMIC SINGLE CELL,PAIRED,0,0,ILLUMINA,Illumina NovaSeq 6000,SRP446371,PRJNA988806,3,988806,SRS18093899,SAMN36028297,simple,10090,Mus musculus,GSM7518069,,,,,,,no,,,,,"LABORATORY OF CELLULAR METABOLISM AND METABOLIC REGULATION, VIB-KU LEUVEN CENTER FOR CANCER BIOLOGY, VIB/KU LEUVEN",SRA1663699,,public,07FB912346833E77F21C3F0D0C3B8935,C6ECC1BDE321FD04338FFC225F6EBF73
We can also get csv output using sra-db-be API, which is more efficient for fetching large number of records:
base = "https://trace.ncbi.nlm.nih.gov/Traces/sra-db-be/sra-"
params = {
"WebEnv": links["linksets"][0]["webenv"],
"rettype": "runinfo",
"query_key": links["linksets"][0]["linksetdbhistories"][1]["querykey"],
}
response = httpx.get(base, params=params)
response.raise_for_status()
print(response.text)
Run,ReleaseDate,LoadDate,spots,bases,spots_with_mates,avgLength,size_MB,AssemblyName,download_path,Experiment,LibraryName,LibraryStrategy,LibrarySelection,LibrarySource,LibraryLayout,InsertSize,InsertDev,Platform,Model,SRAStudy,BioProject,Study_Pubmed_id,ProjectID,Sample,BioSample,SampleType,TaxID,ScientificName,SampleName,g1k_pop_code,source,g1k_analysis_group,Subject_ID,Sex,Disease,Tumor,Affection_Status,Analyte_Type,Histological_Type,Body_Site,CenterName,Submission,dbgap_study_accession,Consent,RunHash,ReadHash
SRR25056229,2024-10-04 14:39:07,2023-06-28 20:50:33,325016382,38676949458,325016382,119,12466,,https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos4/sra-pub-zq-7/SRR025/25056/SRR25056229/SRR25056229.lite.1,SRX20810432,GSM7518065,RNA-Seq,cDNA,TRANSCRIPTOMIC SINGLE CELL,PAIRED,0,0,ILLUMINA,Illumina NovaSeq 6000,SRP446371,PRJNA988806,3,988806,SRS18093896,SAMN36028301,simple,10090,Mus musculus,GSM7518065,,,,,,,no,,,,,"LABORATORY OF CELLULAR METABOLISM AND METABOLIC REGULATION, VIB-KU LEUVEN CENTER FOR CANCER BIOLOGY, VIB/KU LEUVEN",SRA1663699,,public,12A0013D89E3EA09D732E909D80A4EA0,16565C220BB5BF8C76B09379099F5662
SRR25056228,2024-10-04 14:39:07,2023-06-28 20:52:00,339308480,40377709120,339308480,119,13157,,https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos4/sra-pub-zq-7/SRR025/25056/SRR25056228/SRR25056228.lite.1,SRX20810433,GSM7518066,RNA-Seq,cDNA,TRANSCRIPTOMIC SINGLE CELL,PAIRED,0,0,ILLUMINA,Illumina NovaSeq 6000,SRP446371,PRJNA988806,3,988806,SRS18093897,SAMN36028300,simple,10090,Mus musculus,GSM7518066,,,,,,,no,,,,,"LABORATORY OF CELLULAR METABOLISM AND METABOLIC REGULATION, VIB-KU LEUVEN CENTER FOR CANCER BIOLOGY, VIB/KU LEUVEN",SRA1663699,,public,EF36BDA7FDE7BCB3B903A1CA26F62A1B,81566D41964391F8570324D21223A27A
SRR25056227,2024-10-04 14:39:07,2023-06-28 21:20:29,362167958,43097987002,362167958,119,13803,,https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos4/sra-pub-zq-7/SRR025/25056/SRR25056227/SRR25056227.lite.1,SRX20810434,GSM7518067,RNA-Seq,cDNA,TRANSCRIPTOMIC SINGLE CELL,PAIRED,0,0,ILLUMINA,Illumina NovaSeq 6000,SRP446371,PRJNA988806,3,988806,SRS18093898,SAMN36028299,simple,10090,Mus musculus,GSM7518067,,,,,,,no,,,,,"LABORATORY OF CELLULAR METABOLISM AND METABOLIC REGULATION, VIB-KU LEUVEN CENTER FOR CANCER BIOLOGY, VIB/KU LEUVEN",SRA1663699,,public,6671EE3C3CDAEE4DED10C126D99F2866,1C19A18F04FAC05BCFC819827271AB51
SRR25056226,2024-10-04 14:39:08,2023-06-28 21:26:02,321922508,38308778452,321922508,119,12382,,https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos4/sra-pub-zq-7/SRR025/25056/SRR25056226/SRR25056226.lite.1,SRX20810435,GSM7518068,RNA-Seq,cDNA,TRANSCRIPTOMIC SINGLE CELL,PAIRED,0,0,ILLUMINA,Illumina NovaSeq 6000,SRP446371,PRJNA988806,3,988806,SRS18093900,SAMN36028298,simple,10090,Mus musculus,GSM7518068,,,,,,,no,,,,,"LABORATORY OF CELLULAR METABOLISM AND METABOLIC REGULATION, VIB-KU LEUVEN CENTER FOR CANCER BIOLOGY, VIB/KU LEUVEN",SRA1663699,,public,31E9A4D84C4AFA2EAF45F87434E3FF59,1F37CFEF2DD30C50C859D5B0B39E485B
SRR25056225,2024-10-04 14:39:08,2023-06-28 21:08:06,332639939,39584152741,332639939,119,12714,,https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos4/sra-pub-zq-7/SRR025/25056/SRR25056225/SRR25056225.lite.1,SRX20810436,GSM7518069,RNA-Seq,cDNA,TRANSCRIPTOMIC SINGLE CELL,PAIRED,0,0,ILLUMINA,Illumina NovaSeq 6000,SRP446371,PRJNA988806,3,988806,SRS18093899,SAMN36028297,simple,10090,Mus musculus,GSM7518069,,,,,,,no,,,,,"LABORATORY OF CELLULAR METABOLISM AND METABOLIC REGULATION, VIB-KU LEUVEN CENTER FOR CANCER BIOLOGY, VIB/KU LEUVEN",SRA1663699,,public,07FB912346833E77F21C3F0D0C3B8935,C6ECC1BDE321FD04338FFC225F6EBF73
BioProject to BioSample¶
Next we can try to fetch biosamples linked to this BioProject using the first link:
eutils_link(
dbfrom="bioproject",
db="biosample",
webenv=search_results["esearchresult"]["webenv"],
query_key=search_results["esearchresult"]["querykey"],
)
{
"header": {
"type": "elink",
"version": "0.3"
},
"linksets": [
{
"dbfrom": "bioproject",
"ids": [
"988806"
],
"linksetdbhistories": [
{
"dbto": "biosample",
"linkname": "bioproject_biosample",
"querykey": "5"
},
{
"dbto": "biosample",
"linkname": "bioproject_biosample_all",
"querykey": "6"
}
],
"webenv": "MCID_69f379d2a5849e8d8c0781b5"
}
]
}
We can see that there are two links to BioSample records, one for the linked biosamples and another for all biosamples linked to the BioProject. Let's try to fetch the linked biosamples using the first link:
eutils_summary(
webenv=links["linksets"][0]["webenv"],
query_key=links["linksets"][0]["linksetdbhistories"][0]["querykey"],
db="biosample",
)
{
"header": {
"type": "esummary",
"version": "0.3"
},
"result": {
"uids": [
"36028301",
"36028300",
"36028299",
"36028298",
"36028297"
],
"36028301": {
"uid": "36028301",
"title": "CM1, Lungs from CM Injection, Metastatic Seeding (d11)",
"accession": "SAMN36028301",
"date": "2024/10/04",
"publicationdate": "2024/10/04",
"modificationdate": "2024/10/04",
"organization": "Laboratory of Cellular Metabolism and Metabolic Regulation, VIB-KU Leuven Center for Cancer Biology, VIB/KU Leuven",
"taxonomy": "10090",
"organism": "Mus musculus",
"sourcesample": "BioSample:SAMN36028301",
"sampledata": "<BioSample access=\"public\" publication_date=\"2024-10-04T00:00:00.000\" last_update=\"2024-10-04T14:36:16.933\" submission_date=\"2023-06-28T20:00:08.023\" id=\"36028301\" accession=\"SAMN36028301\"> <Ids> <Id db=\"BioSample\" is_primary=\"1\">SAMN36028301</Id> <Id db=\"SRA\">SRS18093896</Id> <Id db=\"GEO\">GSM7518065</Id> </Ids> <Description> <Title>CM1, Lungs from CM Injection, Metastatic Seeding (d11)</Title> <Organism taxonomy_id=\"10090\" taxonomy_name=\"Mus musculus\"> <OrganismName>Mus musculus</OrganismName> </Organism> </Description> <Owner> <Name>Laboratory of Cellular Metabolism and Metabolic Regulation, VIB-KU Leuven Center for Cancer Biology, VIB/KU Leuven</Name> <Contacts> <Contact> <Name> <First>Juan</First> <Last>Fern\u00e1ndez-Garc\u00eda</Last> </Name> </Contact> </Contacts> </Owner> <Models> <Model>Generic</Model> </Models> <Package display_name=\"Generic\">Generic.1.0</Package> <Attributes> <Attribute attribute_name=\"source_name\" harmonized_name=\"source_name\" display_name=\"source name\">Lung</Attribute> <Attribute attribute_name=\"strain\" harmonized_name=\"strain\" display_name=\"strain\">BALB/c</Attribute> <Attribute attribute_name=\"Sex\" harmonized_name=\"sex\" display_name=\"sex\">female</Attribute> <Attribute attribute_name=\"age\" harmonized_name=\"age\" display_name=\"age\">10 weeks-old</Attribute> <Attribute attribute_name=\"tissue\" harmonized_name=\"tissue\" display_name=\"tissue\">Lung</Attribute> <Attribute attribute_name=\"treatment\" harmonized_name=\"treatment\" display_name=\"treatment\">Control Medium (CM)</Attribute> <Attribute attribute_name=\"injected cell_line\">4T1 CD90.1</Attribute> <Attribute attribute_name=\"metastasis stage\">Seeding (d11)</Attribute> <Attribute attribute_name=\"geo_loc_name\" harmonized_name=\"geo_loc_name\" display_name=\"geographic location\">missing</Attribute> <Attribute attribute_name=\"collection_date\" harmonized_name=\"collection_date\" display_name=\"collection date\">missing</Attribute> </Attributes> <Links> <Link type=\"url\" label=\"GEO Sample GSM7518065\">https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM7518065</Link> <Link type=\"entrez\" target=\"bioproject\" label=\"PRJNA988806\">988806</Link> </Links> <Status status=\"live\" when=\"2024-10-04T14:36:16.933\"/> </BioSample> ",
"identifiers": "BioSample: SAMN36028301; SRA: SRS18093896; GEO: GSM7518065",
"infraspecies": "strain: BALB/c",
"package": "Generic",
"sortkey": 120241004
},
"36028300": {
"uid": "36028300",
"title": "CM2, Lungs from CM Injection, Metastatic Colonization (d16)",
"accession": "SAMN36028300",
"date": "2024/10/04",
"publicationdate": "2024/10/04",
"modificationdate": "2024/10/04",
"organization": "Laboratory of Cellular Metabolism and Metabolic Regulation, VIB-KU Leuven Center for Cancer Biology, VIB/KU Leuven",
"taxonomy": "10090",
"organism": "Mus musculus",
"sourcesample": "BioSample:SAMN36028300",
"sampledata": "<BioSample access=\"public\" publication_date=\"2024-10-04T00:00:00.000\" last_update=\"2024-10-04T14:36:16.816\" submission_date=\"2023-06-28T20:00:07.930\" id=\"36028300\" accession=\"SAMN36028300\"> <Ids> <Id db=\"BioSample\" is_primary=\"1\">SAMN36028300</Id> <Id db=\"SRA\">SRS18093897</Id> <Id db=\"GEO\">GSM7518066</Id> </Ids> <Description> <Title>CM2, Lungs from CM Injection, Metastatic Colonization (d16)</Title> <Organism taxonomy_id=\"10090\" taxonomy_name=\"Mus musculus\"> <OrganismName>Mus musculus</OrganismName> </Organism> </Description> <Owner> <Name>Laboratory of Cellular Metabolism and Metabolic Regulation, VIB-KU Leuven Center for Cancer Biology, VIB/KU Leuven</Name> <Contacts> <Contact> <Name> <First>Juan</First> <Last>Fern\u00e1ndez-Garc\u00eda</Last> </Name> </Contact> </Contacts> </Owner> <Models> <Model>Generic</Model> </Models> <Package display_name=\"Generic\">Generic.1.0</Package> <Attributes> <Attribute attribute_name=\"source_name\" harmonized_name=\"source_name\" display_name=\"source name\">Lung</Attribute> <Attribute attribute_name=\"strain\" harmonized_name=\"strain\" display_name=\"strain\">BALB/c</Attribute> <Attribute attribute_name=\"Sex\" harmonized_name=\"sex\" display_name=\"sex\">female</Attribute> <Attribute attribute_name=\"age\" harmonized_name=\"age\" display_name=\"age\">11 weeks-old</Attribute> <Attribute attribute_name=\"tissue\" harmonized_name=\"tissue\" display_name=\"tissue\">Lung</Attribute> <Attribute attribute_name=\"treatment\" harmonized_name=\"treatment\" display_name=\"treatment\">Control Medium (CM)</Attribute> <Attribute attribute_name=\"injected cell_line\">4T1 CD90.1</Attribute> <Attribute attribute_name=\"metastasis stage\">Colonization (d16)</Attribute> <Attribute attribute_name=\"geo_loc_name\" harmonized_name=\"geo_loc_name\" display_name=\"geographic location\">missing</Attribute> <Attribute attribute_name=\"collection_date\" harmonized_name=\"collection_date\" display_name=\"collection date\">missing</Attribute> </Attributes> <Links> <Link type=\"url\" label=\"GEO Sample GSM7518066\">https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM7518066</Link> <Link type=\"entrez\" target=\"bioproject\" label=\"PRJNA988806\">988806</Link> </Links> <Status status=\"live\" when=\"2024-10-04T14:36:16.816\"/> </BioSample> ",
"identifiers": "BioSample: SAMN36028300; SRA: SRS18093897; GEO: GSM7518066",
"infraspecies": "strain: BALB/c",
"package": "Generic",
"sortkey": 120241004
},
"36028299": {
"uid": "36028299",
"title": "TSF1a, Lungs from TSF Injection, Metastatic Seeding (d11), Replicate a",
"accession": "SAMN36028299",
"date": "2024/10/04",
"publicationdate": "2024/10/04",
"modificationdate": "2024/10/04",
"organization": "Laboratory of Cellular Metabolism and Metabolic Regulation, VIB-KU Leuven Center for Cancer Biology, VIB/KU Leuven",
"taxonomy": "10090",
"organism": "Mus musculus",
"sourcesample": "BioSample:SAMN36028299",
"sampledata": "<BioSample access=\"public\" publication_date=\"2024-10-04T00:00:00.000\" last_update=\"2024-10-04T14:36:16.712\" submission_date=\"2023-06-28T20:00:07.830\" id=\"36028299\" accession=\"SAMN36028299\"> <Ids> <Id db=\"BioSample\" is_primary=\"1\">SAMN36028299</Id> <Id db=\"SRA\">SRS18093898</Id> <Id db=\"GEO\">GSM7518067</Id> </Ids> <Description> <Title>TSF1a, Lungs from TSF Injection, Metastatic Seeding (d11), Replicate a</Title> <Organism taxonomy_id=\"10090\" taxonomy_name=\"Mus musculus\"> <OrganismName>Mus musculus</OrganismName> </Organism> </Description> <Owner> <Name>Laboratory of Cellular Metabolism and Metabolic Regulation, VIB-KU Leuven Center for Cancer Biology, VIB/KU Leuven</Name> <Contacts> <Contact> <Name> <First>Juan</First> <Last>Fern\u00e1ndez-Garc\u00eda</Last> </Name> </Contact> </Contacts> </Owner> <Models> <Model>Generic</Model> </Models> <Package display_name=\"Generic\">Generic.1.0</Package> <Attributes> <Attribute attribute_name=\"source_name\" harmonized_name=\"source_name\" display_name=\"source name\">Lung</Attribute> <Attribute attribute_name=\"strain\" harmonized_name=\"strain\" display_name=\"strain\">BALB/c</Attribute> <Attribute attribute_name=\"Sex\" harmonized_name=\"sex\" display_name=\"sex\">female</Attribute> <Attribute attribute_name=\"age\" harmonized_name=\"age\" display_name=\"age\">10 weeks-old</Attribute> <Attribute attribute_name=\"tissue\" harmonized_name=\"tissue\" display_name=\"tissue\">Lung</Attribute> <Attribute attribute_name=\"treatment\" harmonized_name=\"treatment\" display_name=\"treatment\">Tumor-Secreted Factors (TSF)</Attribute> <Attribute attribute_name=\"injected cell_line\">4T1 CD90.1</Attribute> <Attribute attribute_name=\"metastasis stage\">Seeding (d11)</Attribute> <Attribute attribute_name=\"geo_loc_name\" harmonized_name=\"geo_loc_name\" display_name=\"geographic location\">missing</Attribute> <Attribute attribute_name=\"collection_date\" harmonized_name=\"collection_date\" display_name=\"collection date\">missing</Attribute> </Attributes> <Links> <Link type=\"url\" label=\"GEO Sample GSM7518067\">https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM7518067</Link> <Link type=\"entrez\" target=\"bioproject\" label=\"PRJNA988806\">988806</Link> </Links> <Status status=\"live\" when=\"2024-10-04T14:36:16.712\"/> </BioSample> ",
"identifiers": "BioSample: SAMN36028299; SRA: SRS18093898; GEO: GSM7518067",
"infraspecies": "strain: BALB/c",
"package": "Generic",
"sortkey": 120241004
},
"36028298": {
"uid": "36028298",
"title": "TSF1b, Lungs from TSF Injection, Metastatic Seeding (d11), Replicate b",
"accession": "SAMN36028298",
"date": "2024/10/04",
"publicationdate": "2024/10/04",
"modificationdate": "2024/10/04",
"organization": "Laboratory of Cellular Metabolism and Metabolic Regulation, VIB-KU Leuven Center for Cancer Biology, VIB/KU Leuven",
"taxonomy": "10090",
"organism": "Mus musculus",
"sourcesample": "BioSample:SAMN36028298",
"sampledata": "<BioSample access=\"public\" publication_date=\"2024-10-04T00:00:00.000\" last_update=\"2024-10-04T14:36:16.583\" submission_date=\"2023-06-28T20:00:07.706\" id=\"36028298\" accession=\"SAMN36028298\"> <Ids> <Id db=\"BioSample\" is_primary=\"1\">SAMN36028298</Id> <Id db=\"SRA\">SRS18093900</Id> <Id db=\"GEO\">GSM7518068</Id> </Ids> <Description> <Title>TSF1b, Lungs from TSF Injection, Metastatic Seeding (d11), Replicate b</Title> <Organism taxonomy_id=\"10090\" taxonomy_name=\"Mus musculus\"> <OrganismName>Mus musculus</OrganismName> </Organism> </Description> <Owner> <Name>Laboratory of Cellular Metabolism and Metabolic Regulation, VIB-KU Leuven Center for Cancer Biology, VIB/KU Leuven</Name> <Contacts> <Contact> <Name> <First>Juan</First> <Last>Fern\u00e1ndez-Garc\u00eda</Last> </Name> </Contact> </Contacts> </Owner> <Models> <Model>Generic</Model> </Models> <Package display_name=\"Generic\">Generic.1.0</Package> <Attributes> <Attribute attribute_name=\"source_name\" harmonized_name=\"source_name\" display_name=\"source name\">Lung</Attribute> <Attribute attribute_name=\"strain\" harmonized_name=\"strain\" display_name=\"strain\">BALB/c</Attribute> <Attribute attribute_name=\"Sex\" harmonized_name=\"sex\" display_name=\"sex\">female</Attribute> <Attribute attribute_name=\"age\" harmonized_name=\"age\" display_name=\"age\">10 weeks-old</Attribute> <Attribute attribute_name=\"tissue\" harmonized_name=\"tissue\" display_name=\"tissue\">Lung</Attribute> <Attribute attribute_name=\"treatment\" harmonized_name=\"treatment\" display_name=\"treatment\">Tumor-Secreted Factors (TSF)</Attribute> <Attribute attribute_name=\"injected cell_line\">4T1 CD90.1</Attribute> <Attribute attribute_name=\"metastasis stage\">Seeding (d11)</Attribute> <Attribute attribute_name=\"geo_loc_name\" harmonized_name=\"geo_loc_name\" display_name=\"geographic location\">missing</Attribute> <Attribute attribute_name=\"collection_date\" harmonized_name=\"collection_date\" display_name=\"collection date\">missing</Attribute> </Attributes> <Links> <Link type=\"url\" label=\"GEO Sample GSM7518068\">https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM7518068</Link> <Link type=\"entrez\" target=\"bioproject\" label=\"PRJNA988806\">988806</Link> </Links> <Status status=\"live\" when=\"2024-10-04T14:36:16.583\"/> </BioSample> ",
"identifiers": "BioSample: SAMN36028298; SRA: SRS18093900; GEO: GSM7518068",
"infraspecies": "strain: BALB/c",
"package": "Generic",
"sortkey": 120241004
},
"36028297": {
"uid": "36028297",
"title": "TSF2, Lungs from TSF Injection, Metastatic Colonization (d16)",
"accession": "SAMN36028297",
"date": "2024/10/04",
"publicationdate": "2024/10/04",
"modificationdate": "2024/10/04",
"organization": "Laboratory of Cellular Metabolism and Metabolic Regulation, VIB-KU Leuven Center for Cancer Biology, VIB/KU Leuven",
"taxonomy": "10090",
"organism": "Mus musculus",
"sourcesample": "BioSample:SAMN36028297",
"sampledata": "<BioSample access=\"public\" publication_date=\"2024-10-04T00:00:00.000\" last_update=\"2024-10-04T14:36:16.467\" submission_date=\"2023-06-28T20:00:07.600\" id=\"36028297\" accession=\"SAMN36028297\"> <Ids> <Id db=\"BioSample\" is_primary=\"1\">SAMN36028297</Id> <Id db=\"SRA\">SRS18093899</Id> <Id db=\"GEO\">GSM7518069</Id> </Ids> <Description> <Title>TSF2, Lungs from TSF Injection, Metastatic Colonization (d16)</Title> <Organism taxonomy_id=\"10090\" taxonomy_name=\"Mus musculus\"> <OrganismName>Mus musculus</OrganismName> </Organism> </Description> <Owner> <Name>Laboratory of Cellular Metabolism and Metabolic Regulation, VIB-KU Leuven Center for Cancer Biology, VIB/KU Leuven</Name> <Contacts> <Contact> <Name> <First>Juan</First> <Last>Fern\u00e1ndez-Garc\u00eda</Last> </Name> </Contact> </Contacts> </Owner> <Models> <Model>Generic</Model> </Models> <Package display_name=\"Generic\">Generic.1.0</Package> <Attributes> <Attribute attribute_name=\"source_name\" harmonized_name=\"source_name\" display_name=\"source name\">Lung</Attribute> <Attribute attribute_name=\"strain\" harmonized_name=\"strain\" display_name=\"strain\">BALB/c</Attribute> <Attribute attribute_name=\"Sex\" harmonized_name=\"sex\" display_name=\"sex\">female</Attribute> <Attribute attribute_name=\"age\" harmonized_name=\"age\" display_name=\"age\">11 weeks-old</Attribute> <Attribute attribute_name=\"tissue\" harmonized_name=\"tissue\" display_name=\"tissue\">Lung</Attribute> <Attribute attribute_name=\"treatment\" harmonized_name=\"treatment\" display_name=\"treatment\">Tumor-Secreted Factors (TSF)</Attribute> <Attribute attribute_name=\"injected cell_line\">4T1 CD90.1</Attribute> <Attribute attribute_name=\"metastasis stage\">Colonization (d16)</Attribute> <Attribute attribute_name=\"geo_loc_name\" harmonized_name=\"geo_loc_name\" display_name=\"geographic location\">missing</Attribute> <Attribute attribute_name=\"collection_date\" harmonized_name=\"collection_date\" display_name=\"collection date\">missing</Attribute> </Attributes> <Links> <Link type=\"url\" label=\"GEO Sample GSM7518069\">https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM7518069</Link> <Link type=\"entrez\" target=\"bioproject\" label=\"PRJNA988806\">988806</Link> </Links> <Status status=\"live\" when=\"2024-10-04T14:36:16.467\"/> </BioSample> ",
"identifiers": "BioSample: SAMN36028297; SRA: SRS18093899; GEO: GSM7518069",
"infraspecies": "strain: BALB/c",
"package": "Generic",
"sortkey": 120241004
}
}
}