{
"@context": "/terms/",
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"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS9693BTRP",
"aliases": [
"bradley-bernstein:scRNA Lib 75",
"buenrostro-bernstein:scRNA Lib 75"
],
"assay_term": {
"@id": "/assay-terms/OBI_0002631/",
"assay_slims": [
"gene expression"
],
"status": "released",
"term_name": "single-cell RNA sequencing assay"
},
"audit": {
"INTERNAL_ACTION": [
{
"category": "mismatched status",
"detail": "Released measurement set [IGVFDS9693BTRP](/measurement-sets/IGVFDS9693BTRP/) has in progress subobject tabular file [IGVFFI0400MBIM](/tabular-files/IGVFFI0400MBIM/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS9693BTRP/"
}
],
"WARNING": [
{
"category": "missing age",
"detail": "Tissue [IGVFSM8719IQYM](/tissues/IGVFSM8719IQYM/) 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/IGVFSM8719IQYM/"
}
]
},
"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": "2023-08-28T17:58:18.519876+00:00",
"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",
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"buenrostro-bernstein:SS-LS_1984_R1",
"buenrostro-bernstein:SS-LS_60_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-08-28T18:21:00.823565+00:00",
"file_format": "fastq",
"file_size": 631222816,
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"s3_uri": "s3://igvf-files/2023/08/28/78301029-441d-4ed6-98f6-33653b78219a/IGVFFI8347HEET.fastq.gz",
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"status": "released",
"term_name": "Illumina NovaSeq 6000"
},
"status": "released",
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2540DVGH/",
"accession": "IGVFFI2540DVGH",
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"bradley-bernstein:SS-LS_60_R2",
"buenrostro-bernstein:SS-LS_1984_R2",
"buenrostro-bernstein:SS-LS_60_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-08-28T18:21:01.814470+00:00",
"file_format": "fastq",
"file_size": 1132730816,
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"s3_uri": "s3://igvf-files/2023/08/28/15d9f827-7217-4059-a9a8-773cf6f5fc1a/IGVFFI2540DVGH.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-137_L1_SS-PKR-130_2022-APRIL-R1-PLATE2-ENTIRE-PLATE_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4227ZFZB/",
"accession": "IGVFFI4227ZFZB",
"aliases": [
"bradley-bernstein:SS-LS_2012_R2",
"bradley-bernstein:SS-LS_244_R2",
"buenrostro-bernstein:SS-LS_2012_R2",
"buenrostro-bernstein:SS-LS_244_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-08-28T18:21:05.422848+00:00",
"file_format": "fastq",
"file_size": 1133956248,
"href": "/sequence-files/IGVFFI4227ZFZB/@@download/IGVFFI4227ZFZB.fastq.gz",
"s3_uri": "s3://igvf-files/2023/08/28/7787418d-2fcc-4cf8-bda2-5ebbe87d35a0/IGVFFI4227ZFZB.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-137_L2_SS-PKR-130_2022-APRIL-R1-PLATE2-ENTIRE-PLATE_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3851WKAQ/",
"accession": "IGVFFI3851WKAQ",
"aliases": [
"bradley-bernstein:SS-LS_2012_R1",
"bradley-bernstein:SS-LS_244_R1",
"buenrostro-bernstein:SS-LS_2012_R1",
"buenrostro-bernstein:SS-LS_244_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-08-28T18:21:04.493648+00:00",
"file_format": "fastq",
"file_size": 631205750,
"href": "/sequence-files/IGVFFI3851WKAQ/@@download/IGVFFI3851WKAQ.fastq.gz",
"s3_uri": "s3://igvf-files/2023/08/28/11a373d2-b564-423e-a482-9fc777332190/IGVFFI3851WKAQ.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-137_L2_SS-PKR-130_2022-APRIL-R1-PLATE2-ENTIRE-PLATE_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI6966IHGR/",
"accession": "IGVFFI6966IHGR",
"aliases": [
"buenrostro-bernstein:SS-LS_2012_seqspec"
],
"content_type": "seqspec",
"creation_timestamp": "2024-09-17T22:50:38.746287+00:00",
"file_format": "yaml",
"file_size": 1230,
"href": "/configuration-files/IGVFFI6966IHGR/@@download/IGVFFI6966IHGR.yaml.gz",
"s3_uri": "s3://igvf-files/2024/09/17/13b705ec-0ad2-4a6b-987b-9d2a69b9889c/IGVFFI6966IHGR.yaml.gz",
"status": "released",
"submitted_file_name": "gs://sw-igvf-submission/seqspec-v3/SS-LS_2012_seqspecv3.yaml.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI8231RUQE/",
"accession": "IGVFFI8231RUQE",
"aliases": [
"buenrostro-bernstein:SS-LS_1984_seqspec"
],
"content_type": "seqspec",
"creation_timestamp": "2024-09-17T22:50:45.352885+00:00",
"file_format": "yaml",
"file_size": 1227,
"href": "/configuration-files/IGVFFI8231RUQE/@@download/IGVFFI8231RUQE.yaml.gz",
"s3_uri": "s3://igvf-files/2024/09/17/4f9262fe-de4d-42f9-ae09-6da00eea23e5/IGVFFI8231RUQE.yaml.gz",
"status": "released",
"submitted_file_name": "gs://sw-igvf-submission/seqspec-v3/SS-LS_1984_seqspecv3.yaml.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS0635KHHW/"
],
"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/IGVFDS3032KHHX/",
"accession": "IGVFDS3032KHHX",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS8556WPGM/",
"accession": "IGVFDS8556WPGM",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS0877CWMW/",
"accession": "IGVFDS0877CWMW",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS4704VICJ/",
"accession": "IGVFDS4704VICJ",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS6361NSJR/",
"accession": "IGVFDS6361NSJR",
"status": "released"
}
],
"release_timestamp": "2025-03-28T21:18:51.263366+00:00",
"samples": [
{
"@id": "/tissues/IGVFSM8719IQYM/",
"@type": [
"Tissue",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM8719IQYM",
"aliases": [
"bradley-bernstein:BioSam 4561_SS-PKR 130",
"buenrostro-bernstein:BioSam 4561_SS-PKR 130"
],
"cellular_sub_pool": "SS-PKR 130",
"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 130)",
"taxa": "Mus musculus"
}
],
"schema_version": "26",
"status": "released",
"submitted_by": {
"@id": "/users/c0838247-5022-46cf-a8fa-426e73bf4c94/",
"title": "Siddarth Wekhande"
},
"submitted_files_timestamp": "2023-08-28T18:21:00.823565+00:00",
"summary": "single-cell RNA sequencing assay (SHARE-seq)",
"uuid": "1ede0e33-ce43-47a0-bd35-ae7379c473e1"
}