{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS8535JZRF/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS8535JZRF",
"aliases": [
"bradley-bernstein:scRNA Lib 70",
"buenrostro-bernstein:scRNA Lib 70"
],
"assay_term": {
"@id": "/assay-terms/OBI_0002631/",
"assay_slims": [
"gene expression"
],
"status": "released",
"term_name": "single-cell RNA sequencing assay"
},
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing publication",
"detail": "Tissue [IGVFSM3932SXVT](/tissues/IGVFSM3932SXVT/) 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/IGVFSM3932SXVT/"
},
{
"category": "missing publication",
"detail": "Measurement set [IGVFDS8535JZRF](/measurement-sets/IGVFDS8535JZRF/) 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": "/measurement-sets/IGVFDS8535JZRF/"
},
{
"category": "mismatched status",
"detail": "Released measurement set [IGVFDS8535JZRF](/measurement-sets/IGVFDS8535JZRF/) has in progress subobject tabular file [IGVFFI0400MBIM](/tabular-files/IGVFFI0400MBIM/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS8535JZRF/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing strand specificity",
"detail": "Measurement set [IGVFDS8535JZRF](/measurement-sets/IGVFDS8535JZRF/) is missing required `strand_specificity`. Gene expression based assays are expected to specify strand specificity.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_missing_strand_specificity",
"path": "/measurement-sets/IGVFDS8535JZRF/"
}
],
"WARNING": [
{
"category": "missing age",
"detail": "Tissue [IGVFSM3932SXVT](/tissues/IGVFSM3932SXVT/) 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/IGVFSM3932SXVT/"
}
]
},
"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": "2023-08-28T20:29:08.014181+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"
}
],
"externally_hosted": false,
"file_set_type": "experimental data",
"files": [
{
"@id": "/sequence-files/IGVFFI3275ZYCM/",
"accession": "IGVFFI3275ZYCM",
"aliases": [
"bradley-bernstein:SS-LS_1979_R2",
"bradley-bernstein:SS-LS_65_R2",
"buenrostro-bernstein:SS-LS_1979_R2",
"buenrostro-bernstein:SS-LS_65_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-09-05T19:27:51.935932+00:00",
"file_format": "fastq",
"file_size": 725043165,
"href": "/sequence-files/IGVFFI3275ZYCM/@@download/IGVFFI3275ZYCM.fastq.gz",
"md5sum": "daf78fb5669167f646aa56328a314244",
"s3_uri": "s3://igvf-files/2023/09/05/06d7979b-38b7-4230-8ee2-dd2240e8d0c6/IGVFFI3275ZYCM.fastq.gz",
"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NovaSeq 6000"
},
"status": "released",
"submitted_file_name": "gs://broad-epi-ss-lane-subsets/SS-CoPA-132_L1_SS-PKR-129_SS-V1-RIGHT-HALF_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4748IHHC/",
"accession": "IGVFFI4748IHHC",
"aliases": [
"bradley-bernstein:SS-LS_1979_R1",
"bradley-bernstein:SS-LS_65_R1",
"buenrostro-bernstein:SS-LS_1979_R1",
"buenrostro-bernstein:SS-LS_65_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-09-05T19:27:50.904320+00:00",
"file_format": "fastq",
"file_size": 406860916,
"href": "/sequence-files/IGVFFI4748IHHC/@@download/IGVFFI4748IHHC.fastq.gz",
"md5sum": "391f3b9b6331475a206d43715c2b8949",
"s3_uri": "s3://igvf-files/2023/09/05/684552ea-4ac4-4bc7-b875-41061175e560/IGVFFI4748IHHC.fastq.gz",
"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NovaSeq 6000"
},
"status": "released",
"submitted_file_name": "gs://broad-epi-ss-lane-subsets/SS-CoPA-132_L1_SS-PKR-129_SS-V1-RIGHT-HALF_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5191KEYH/",
"accession": "IGVFFI5191KEYH",
"aliases": [
"bradley-bernstein:SS-LS_2007_R1",
"bradley-bernstein:SS-LS_249_R1",
"buenrostro-bernstein:SS-LS_2007_R1",
"buenrostro-bernstein:SS-LS_249_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-09-05T19:28:09.595949+00:00",
"file_format": "fastq",
"file_size": 406574971,
"href": "/sequence-files/IGVFFI5191KEYH/@@download/IGVFFI5191KEYH.fastq.gz",
"md5sum": "c24d74e5d20f386c59f38be0f030b3a8",
"s3_uri": "s3://igvf-files/2023/09/05/cef2f417-1373-4980-b8a6-740a116ffded/IGVFFI5191KEYH.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008637/",
"status": "released",
"term_name": "Illumina NovaSeq 6000"
},
"status": "released",
"submitted_file_name": "gs://broad-epi-ss-lane-subsets/SS-CoPA-132_L2_SS-PKR-129_SS-V1-RIGHT-HALF_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2756OYVG/",
"accession": "IGVFFI2756OYVG",
"aliases": [
"bradley-bernstein:SS-LS_2007_R2",
"bradley-bernstein:SS-LS_249_R2",
"buenrostro-bernstein:SS-LS_2007_R2",
"buenrostro-bernstein:SS-LS_249_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-09-05T19:28:10.480786+00:00",
"file_format": "fastq",
"file_size": 725619073,
"href": "/sequence-files/IGVFFI2756OYVG/@@download/IGVFFI2756OYVG.fastq.gz",
"md5sum": "705c83dc67a5de19520b2deffab66cb7",
"s3_uri": "s3://igvf-files/2023/09/05/88d27fd3-d9da-4831-a06d-64c0a85e9523/IGVFFI2756OYVG.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008637/",
"status": "released",
"term_name": "Illumina NovaSeq 6000"
},
"status": "released",
"submitted_file_name": "gs://broad-epi-ss-lane-subsets/SS-CoPA-132_L2_SS-PKR-129_SS-V1-RIGHT-HALF_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI2090VQMW/",
"accession": "IGVFFI2090VQMW",
"aliases": [
"buenrostro-bernstein:SS-LS_2007_seqspec"
],
"content_type": "seqspec",
"creation_timestamp": "2024-09-17T22:50:44.270667+00:00",
"file_format": "yaml",
"file_size": 1228,
"href": "/configuration-files/IGVFFI2090VQMW/@@download/IGVFFI2090VQMW.yaml.gz",
"md5sum": "bc9d0870b7693715b7453247d6eafa9c",
"s3_uri": "s3://igvf-files/2024/09/17/0f9fc998-847b-4407-b4f5-7486063e2dc7/IGVFFI2090VQMW.yaml.gz",
"status": "released",
"submitted_file_name": "gs://sw-igvf-submission/seqspec-v3/SS-LS_2007_seqspecv3.yaml.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI8780GOTT/",
"accession": "IGVFFI8780GOTT",
"aliases": [
"buenrostro-bernstein:SS-LS_1979_seqspec"
],
"content_type": "seqspec",
"creation_timestamp": "2024-09-17T22:50:50.853680+00:00",
"file_format": "yaml",
"file_size": 1230,
"href": "/configuration-files/IGVFFI8780GOTT/@@download/IGVFFI8780GOTT.yaml.gz",
"md5sum": "34d17c4a8d48d722c67bec4d7d73925d",
"s3_uri": "s3://igvf-files/2024/09/17/f732ecdf-f8de-4471-ad64-92e7c14cdc35/IGVFFI8780GOTT.yaml.gz",
"status": "released",
"submitted_file_name": "gs://sw-igvf-submission/seqspec-v3/SS-LS_1979_seqspecv3.yaml.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS8415FVDT/"
],
"lab": {
"@id": "/labs/jason-buenrostro/",
"title": "Jason Buenrostro, Broad"
},
"multiome_size": 6,
"notes": "Preferred_assay_titles enum SHARE-Seq has been renamed to be SHARE-seq.",
"onlist_files": [
"/tabular-files/IGVFFI0400MBIM/"
],
"onlist_method": "multi",
"preferred_assay_title": "SHARE-seq",
"protocols": [
"https://www.protocols.io/view/share-seq-protocol-v2-2-di3y4gpw"
],
"related_multiome_datasets": [
{
"@id": "/measurement-sets/IGVFDS0020LQRY/",
"accession": "IGVFDS0020LQRY",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS5192VPKQ/",
"accession": "IGVFDS5192VPKQ",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS4911ZDCJ/",
"accession": "IGVFDS4911ZDCJ",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS3638UVNV/",
"accession": "IGVFDS3638UVNV",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS8078FJZR/",
"accession": "IGVFDS8078FJZR",
"status": "released"
}
],
"release_timestamp": "2025-03-28T21:22:46.046784+00:00",
"samples": [
{
"@id": "/tissues/IGVFSM3932SXVT/",
"@type": [
"Tissue",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM3932SXVT",
"aliases": [
"bradley-bernstein:BioSam 4561_SS-PKR 129",
"buenrostro-bernstein:BioSam 4561_SS-PKR 129"
],
"cellular_sub_pool": "SS-PKR 129",
"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 129)",
"taxa": "Mus musculus"
}
],
"schema_version": "26",
"status": "released",
"submitted_by": {
"@id": "/users/c0838247-5022-46cf-a8fa-426e73bf4c94/",
"title": "Siddarth Wekhande"
},
"submitted_files_timestamp": "2023-09-05T19:27:50.904320+00:00",
"summary": "single-cell RNA sequencing assay (SHARE-seq)",
"uuid": "45f9f765-15f0-495e-80e8-16d9e5ca361b"
}