{
"@context": "/terms/",
"@id": "/analysis-sets/IGVFDS4769QTGM/",
"@type": [
"AnalysisSet",
"FileSet",
"Item"
],
"accession": "IGVFDS4769QTGM",
"aliases": [
"buenrostro-bernstein:AnalysisSet_BioSam-4561_SS-PKR-132"
],
"assay_titles": [
"SHARE-seq"
],
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing publication",
"detail": "Tissue [IGVFSM8883WYCA](/tissues/IGVFSM8883WYCA/) has no `publications`. Released and archived samples are expected to be associated with a publication.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_sample_missing_publication",
"path": "/tissues/IGVFSM8883WYCA/"
},
{
"category": "missing publication",
"detail": "Analysis set [IGVFDS4769QTGM](/analysis-sets/IGVFDS4769QTGM/) has no `publications`. Released and archived file sets are expected to be associated with a publication.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_file_set_missing_publication",
"path": "/analysis-sets/IGVFDS4769QTGM/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing reference files",
"detail": "Analysis set [IGVFDS4769QTGM](/analysis-sets/IGVFDS4769QTGM/) has file(s) with no transcriptome `reference_files`: [IGVFFI1698LKKR](/alignment-files/IGVFFI1698LKKR/) Analysis set files processed from transcript sequence data are expected to link to a transcriptome reference.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_missing_transcriptome",
"path": "/analysis-sets/IGVFDS4769QTGM/"
}
],
"WARNING": [
{
"category": "missing age",
"detail": "Tissue [IGVFSM8883WYCA](/tissues/IGVFSM8883WYCA/) is missing `upper_bound_age`, `lower_bound_age`, and `age_units`. Tissues, primary cells, and whole organisms are expected to specify a lower bound age, upper bound age, and age units.",
"level": 40,
"level_name": "WARNING",
"name": "audit_biosample_age",
"path": "/tissues/IGVFSM8883WYCA/"
}
]
},
"award": {
"@id": "/awards/HG011986/",
"component": "mapping",
"contact_pi": {
"@id": "/users/33c6eb70-e143-4f77-9661-4b3905737daa/",
"title": "Jason Buenrostro"
},
"title": "A foundational resource of functional elements, TF footprints and gene regulatory interactions"
},
"control_for": [],
"creation_timestamp": "2025-03-18T19:13:52.687180+00:00",
"data_use_limitation_summaries": [
"no certificate"
],
"donors": [
{
"@id": "/rodent-donors/IGVFDO1318PLKS/",
"accession": "IGVFDO1318PLKS",
"aliases": [
"bradley-bernstein:Donor 1503",
"buenrostro-bernstein:Donor 1503"
],
"sex": "female",
"status": "released",
"taxa": "Mus musculus"
}
],
"file_set_type": "intermediate analysis",
"files": [
{
"@id": "/matrix-files/IGVFFI8115NBJO/",
"accession": "IGVFFI8115NBJO",
"aliases": [
"buenrostro-bernstein:IGVFDS4769QTGM_matrix_file"
],
"content_type": "sparse gene count matrix",
"creation_timestamp": "2025-03-27T00:20:09.307266+00:00",
"derived_from": [
"/sequence-files/IGVFFI9532ANKQ/",
"/sequence-files/IGVFFI7523TEDF/",
"/sequence-files/IGVFFI3892BRSH/",
"/sequence-files/IGVFFI0281YHNG/",
"/sequence-files/IGVFFI7687JKNF/",
"/sequence-files/IGVFFI5244UXCI/",
"/sequence-files/IGVFFI4275DDIL/",
"/sequence-files/IGVFFI6803APEV/",
"/sequence-files/IGVFFI3335XFSL/",
"/sequence-files/IGVFFI4886JZDI/",
"/sequence-files/IGVFFI9060BQTU/",
"/sequence-files/IGVFFI4287WIUQ/",
"/configuration-files/IGVFFI1891JLQU/",
"/configuration-files/IGVFFI9218ORYZ/",
"/configuration-files/IGVFFI7278ACIY/",
"/configuration-files/IGVFFI2395FWQZ/",
"/configuration-files/IGVFFI8545GMTZ/",
"/configuration-files/IGVFFI2472NKBH/"
],
"file_format": "h5ad",
"file_size": 961613920,
"href": "/matrix-files/IGVFFI8115NBJO/@@download/IGVFFI8115NBJO.h5ad",
"md5sum": "bfb58932ff34d9966e13ec5d62efad35",
"s3_uri": "s3://igvf-files/2025/03/27/77dc3e2e-e4b3-45aa-b9ec-d5cf2a64fb7d/IGVFFI8115NBJO.h5ad",
"status": "released",
"submitted_file_name": "gs://fc-9649faf8-a4ec-4ca4-a975-498a1707d03c/submissions/a6d4a8e2-651e-421f-ae34-bfdf4cf1f42e/single_cell_pipeline/e5388b35-8930-49ab-a59f-e57e72b28278/call-rna/wf_rna/ee10e6d6-0bbd-468a-8de3-f27d3232336b/call-kb/SS-PKR-132.h5ad",
"upload_status": "validated"
},
{
"@id": "/tabular-files/IGVFFI6914SBPN/",
"accession": "IGVFFI6914SBPN",
"aliases": [
"buenrostro-bernstein:IGVFDS4769QTGM_fragments"
],
"assembly": "GRCm39",
"content_type": "fragments",
"controlled_access": false,
"creation_timestamp": "2025-03-27T01:18:16.514140+00:00",
"derived_from": [
"/sequence-files/IGVFFI9201WYHO/",
"/sequence-files/IGVFFI0137ERGS/",
"/sequence-files/IGVFFI7270DMRN/",
"/sequence-files/IGVFFI0086MOYB/",
"/sequence-files/IGVFFI3794YMRL/",
"/sequence-files/IGVFFI4498HQPP/",
"/sequence-files/IGVFFI9305UBWA/",
"/sequence-files/IGVFFI3119TNSE/",
"/sequence-files/IGVFFI7385RIWV/",
"/sequence-files/IGVFFI0043UUDP/",
"/sequence-files/IGVFFI2302SLNH/",
"/sequence-files/IGVFFI1728ECQN/",
"/configuration-files/IGVFFI5361AABQ/",
"/configuration-files/IGVFFI0846TMYA/",
"/configuration-files/IGVFFI3071NXZT/",
"/configuration-files/IGVFFI6768ERPY/",
"/configuration-files/IGVFFI8541ZMMO/",
"/configuration-files/IGVFFI8780JHZV/"
],
"file_format": "bed",
"file_size": 845479534,
"href": "/tabular-files/IGVFFI6914SBPN/@@download/IGVFFI6914SBPN.bed.gz",
"md5sum": "bca285b25bdd46360508aec5025606ea",
"s3_uri": "s3://igvf-files/2025/03/27/8345faa8-5876-4c04-9854-60c7b99684c9/IGVFFI6914SBPN.bed.gz",
"status": "released",
"submitted_file_name": "gs://fc-9649faf8-a4ec-4ca4-a975-498a1707d03c/submissions/a6d4a8e2-651e-421f-ae34-bfdf4cf1f42e/single_cell_pipeline/e5388b35-8930-49ab-a59f-e57e72b28278/call-atac/wf_atac/60c7c6a3-129f-4fff-90da-9ddb46c5b409/call-generate_fragments/SS-PKR-132.fragments.tsv.gz",
"upload_status": "validated"
},
{
"@id": "/alignment-files/IGVFFI1698LKKR/",
"accession": "IGVFFI1698LKKR",
"aliases": [
"buenrostro-bernstein:IGVFDS4769QTGM_bam"
],
"assembly": "GRCm39",
"content_type": "alignments",
"controlled_access": false,
"creation_timestamp": "2025-03-27T01:06:05.817112+00:00",
"derived_from": [
"/sequence-files/IGVFFI9201WYHO/",
"/sequence-files/IGVFFI0137ERGS/",
"/sequence-files/IGVFFI7270DMRN/",
"/sequence-files/IGVFFI0086MOYB/",
"/sequence-files/IGVFFI3794YMRL/",
"/sequence-files/IGVFFI4498HQPP/",
"/sequence-files/IGVFFI9305UBWA/",
"/sequence-files/IGVFFI3119TNSE/",
"/sequence-files/IGVFFI7385RIWV/",
"/sequence-files/IGVFFI0043UUDP/",
"/sequence-files/IGVFFI2302SLNH/",
"/sequence-files/IGVFFI1728ECQN/",
"/configuration-files/IGVFFI5361AABQ/",
"/configuration-files/IGVFFI0846TMYA/",
"/configuration-files/IGVFFI3071NXZT/",
"/configuration-files/IGVFFI6768ERPY/",
"/configuration-files/IGVFFI8541ZMMO/",
"/configuration-files/IGVFFI8780JHZV/"
],
"file_format": "bam",
"file_size": 6099937018,
"href": "/alignment-files/IGVFFI1698LKKR/@@download/IGVFFI1698LKKR.bam",
"md5sum": "f1635fe03048bef913038bbe99975479",
"s3_uri": "s3://igvf-files/2025/03/27/f1825d7a-e839-467d-91fe-c3860b3c96b7/IGVFFI1698LKKR.bam",
"status": "released",
"submitted_file_name": "gs://fc-9649faf8-a4ec-4ca4-a975-498a1707d03c/submissions/a6d4a8e2-651e-421f-ae34-bfdf4cf1f42e/single_cell_pipeline/e5388b35-8930-49ab-a59f-e57e72b28278/call-atac/wf_atac/60c7c6a3-129f-4fff-90da-9ddb46c5b409/call-generate_bam/SS-PKR-132.bam",
"upload_status": "validated"
},
{
"@id": "/index-files/IGVFFI0917ETKY/",
"accession": "IGVFFI0917ETKY",
"aliases": [
"buenrostro-bernstein:IGVFDS4769QTGM_fragment_index"
],
"assembly": "GRCm39",
"content_type": "index",
"controlled_access": false,
"creation_timestamp": "2025-03-27T01:21:06.351989+00:00",
"derived_from": [
"/tabular-files/IGVFFI6914SBPN/"
],
"file_format": "tbi",
"file_size": 679653,
"href": "/index-files/IGVFFI0917ETKY/@@download/IGVFFI0917ETKY.tbi",
"md5sum": "0924babedab5ab22e40e6770c4798cf5",
"s3_uri": "s3://igvf-files/2025/03/27/5da6809a-d640-4204-87f6-defc98114006/IGVFFI0917ETKY.tbi",
"status": "released",
"submitted_file_name": "gs://fc-9649faf8-a4ec-4ca4-a975-498a1707d03c/submissions/a6d4a8e2-651e-421f-ae34-bfdf4cf1f42e/single_cell_pipeline/e5388b35-8930-49ab-a59f-e57e72b28278/call-atac/wf_atac/60c7c6a3-129f-4fff-90da-9ddb46c5b409/call-generate_fragments/SS-PKR-132.fragments.tsv.gz.tbi",
"upload_status": "validated"
},
{
"@id": "/index-files/IGVFFI5318ADUO/",
"accession": "IGVFFI5318ADUO",
"aliases": [
"buenrostro-bernstein:IGVFDS4769QTGM_bam_index"
],
"assembly": "GRCm39",
"content_type": "index",
"controlled_access": false,
"creation_timestamp": "2025-03-27T04:43:24.779629+00:00",
"derived_from": [
"/alignment-files/IGVFFI1698LKKR/"
],
"file_format": "bai",
"file_size": 2746376,
"href": "/index-files/IGVFFI5318ADUO/@@download/IGVFFI5318ADUO.bai",
"md5sum": "fe1ba44d498643ca81f1bce671957a9c",
"s3_uri": "s3://igvf-files/2025/03/27/6d500cd0-36e5-4619-88b5-be48b13b4bed/IGVFFI5318ADUO.bai",
"status": "released",
"submitted_file_name": "gs://fc-9649faf8-a4ec-4ca4-a975-498a1707d03c/submissions/03d491e0-13b3-4b9d-89ce-ae4ebc4c6939/samtools_index_workflow/b2c77a10-4f47-4413-854d-116f35c23fb6/call-samtools_index/SS-PKR-132.bam.bai",
"upload_status": "validated"
},
{
"@id": "/matrix-files/IGVFFI3859IJXZ/",
"accession": "IGVFFI3859IJXZ",
"aliases": [
"buenrostro-bernstein:IGVFDS4769QTGM_rna_kb_output_folder_tar_gz"
],
"content_type": "comprehensive gene count matrix",
"creation_timestamp": "2025-04-01T16:24:27.531332+00:00",
"derived_from": [
"/sequence-files/IGVFFI9532ANKQ/",
"/sequence-files/IGVFFI7523TEDF/",
"/sequence-files/IGVFFI3892BRSH/",
"/sequence-files/IGVFFI0281YHNG/",
"/sequence-files/IGVFFI7687JKNF/",
"/sequence-files/IGVFFI5244UXCI/",
"/sequence-files/IGVFFI4275DDIL/",
"/sequence-files/IGVFFI6803APEV/",
"/sequence-files/IGVFFI3335XFSL/",
"/sequence-files/IGVFFI4886JZDI/",
"/sequence-files/IGVFFI9060BQTU/",
"/sequence-files/IGVFFI4287WIUQ/",
"/configuration-files/IGVFFI1891JLQU/",
"/configuration-files/IGVFFI9218ORYZ/",
"/configuration-files/IGVFFI7278ACIY/",
"/configuration-files/IGVFFI2395FWQZ/",
"/configuration-files/IGVFFI8545GMTZ/",
"/configuration-files/IGVFFI2472NKBH/"
],
"file_format": "tar",
"file_size": 5242691479,
"href": "/matrix-files/IGVFFI3859IJXZ/@@download/IGVFFI3859IJXZ.tar.gz",
"md5sum": "892e475cb77d95472d1485f1c8646a1d",
"s3_uri": "s3://igvf-files/2025/04/01/816ac26a-7778-4686-ba42-c09e3815d0dd/IGVFFI3859IJXZ.tar.gz",
"status": "released",
"submitted_file_name": "gs://fc-9649faf8-a4ec-4ca4-a975-498a1707d03c/submissions/a6d4a8e2-651e-421f-ae34-bfdf4cf1f42e/single_cell_pipeline/e5388b35-8930-49ab-a59f-e57e72b28278/call-rna/wf_rna/ee10e6d6-0bbd-468a-8de3-f27d3232336b/call-kb/SS-PKR-132.tar.gz",
"upload_status": "validated"
}
],
"functional_assay_mechanisms": [],
"input_file_sets": [
{
"@id": "/measurement-sets/IGVFDS8700PWZJ/",
"accession": "IGVFDS8700PWZJ",
"aliases": [
"bradley-bernstein:scATAC Lib 120",
"buenrostro-bernstein:scATAC Lib 120"
],
"file_set_type": "experimental data",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS9728TWXO/",
"accession": "IGVFDS9728TWXO",
"aliases": [
"bradley-bernstein:scATAC Lib 119",
"buenrostro-bernstein:scATAC Lib 119"
],
"file_set_type": "experimental data",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS7747XDUI/",
"accession": "IGVFDS7747XDUI",
"aliases": [
"bradley-bernstein:scATAC Lib 118",
"buenrostro-bernstein:scATAC Lib 118"
],
"file_set_type": "experimental data",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS6721DTCZ/",
"accession": "IGVFDS6721DTCZ",
"aliases": [
"bradley-bernstein:scRNA Lib 129",
"buenrostro-bernstein:scRNA Lib 129"
],
"file_set_type": "experimental data",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS4161OUYL/",
"accession": "IGVFDS4161OUYL",
"aliases": [
"bradley-bernstein:scRNA Lib 128",
"buenrostro-bernstein:scRNA Lib 128"
],
"file_set_type": "experimental data",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS9620KXMW/",
"accession": "IGVFDS9620KXMW",
"aliases": [
"bradley-bernstein:scRNA Lib 127",
"buenrostro-bernstein:scRNA Lib 127"
],
"file_set_type": "experimental data",
"status": "released"
}
],
"input_for": [],
"lab": {
"@id": "/labs/jason-buenrostro/",
"title": "Jason Buenrostro, Broad"
},
"protocols": [
"https://www.protocols.io/view/share-seq-protocol-v2-2-di3y4gpw"
],
"release_timestamp": "2025-05-07T20:35:00.612332+00:00",
"sample_summary": "Mus musculus brain tissue",
"samples": [
{
"@id": "/tissues/IGVFSM8883WYCA/",
"@type": [
"Tissue",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM8883WYCA",
"aliases": [
"bradley-bernstein:BioSam 4561_SS-PKR 132",
"buenrostro-bernstein:BioSam 4561_SS-PKR 132"
],
"cellular_sub_pool": "SS-PKR 132",
"classifications": [
"tissue"
],
"institutional_certificates": [],
"sample_terms": [
{
"@id": "/sample-terms/UBERON_0000955/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"status": "released",
"summary": "brain",
"term_name": "brain"
}
],
"status": "released",
"summary": "Mus musculus C57BL/6 (female) brain tissue (cellular sub pool: SS-PKR 132)",
"taxa": "Mus musculus"
}
],
"schema_version": "9",
"status": "released",
"submitted_by": {
"@id": "/users/c0838247-5022-46cf-a8fa-426e73bf4c94/",
"title": "Siddarth Wekhande"
},
"submitted_files_timestamp": "2025-03-27T00:20:09.307266+00:00",
"summary": "single-cell ATAC-seq (SHARE-seq), single-cell RNA sequencing assay (SHARE-seq)",
"uuid": "d7009a4d-dbdc-4b9b-95a4-a35cdff425d5",
"workflows": [
{
"@id": "/workflows/IGVFWF7365VWQV/",
"accession": "IGVFWF7365VWQV",
"name": "igvf single cell uniform pipeline",
"status": "in progress",
"uniform_pipeline": true
}
]
}