{
"@context": "/terms/",
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"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS3032KHHX",
"aliases": [
"bradley-bernstein:scATAC Lib 113",
"buenrostro-bernstein:scATAC Lib 113"
],
"assay_term": {
"@id": "/assay-terms/OBI_0002764/",
"assay_slims": [
"chromatin accessibility"
],
"status": "released",
"term_name": "single-cell ATAC-seq"
},
"audit": {
"INTERNAL_ACTION": [
{
"category": "mismatched status",
"detail": "Released measurement set [IGVFDS3032KHHX](/measurement-sets/IGVFDS3032KHHX/) has in progress subobject tabular file [IGVFFI0400MBIM](/tabular-files/IGVFFI0400MBIM/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS3032KHHX/"
}
],
"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": "2023-08-28T17:58:19.041452+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",
"files": [
{
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"accession": "IGVFFI4386BDER",
"aliases": [
"bradley-bernstein:SS-LS_2005_R2",
"bradley-bernstein:SS-LS_39_R2",
"buenrostro-bernstein:SS-LS_2005_R2",
"buenrostro-bernstein:SS-LS_39_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-08-28T18:21:07.331449+00:00",
"file_format": "fastq",
"file_size": 211585168,
"href": "/sequence-files/IGVFFI4386BDER/@@download/IGVFFI4386BDER.fastq.gz",
"s3_uri": "s3://igvf-files/2023/08/28/0550d9ce-c0df-48c5-98ef-0baae5f48fb6/IGVFFI4386BDER.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-158_L1_SS-PKR-130_SS-V1-LEFT-HALF_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7508PACU/",
"accession": "IGVFFI7508PACU",
"aliases": [
"bradley-bernstein:SS-LS_2005_R1",
"bradley-bernstein:SS-LS_39_R1",
"buenrostro-bernstein:SS-LS_2005_R1",
"buenrostro-bernstein:SS-LS_39_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-08-28T18:21:06.450333+00:00",
"file_format": "fastq",
"file_size": 120487060,
"href": "/sequence-files/IGVFFI7508PACU/@@download/IGVFFI7508PACU.fastq.gz",
"s3_uri": "s3://igvf-files/2023/08/28/4bc3040d-8609-498f-9cea-861d6fce67fc/IGVFFI7508PACU.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-158_L1_SS-PKR-130_SS-V1-LEFT-HALF_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2472BMSD/",
"accession": "IGVFFI2472BMSD",
"aliases": [
"bradley-bernstein:SS-LS_2033_R1",
"bradley-bernstein:SS-LS_239_R1",
"buenrostro-bernstein:SS-LS_2033_R1",
"buenrostro-bernstein:SS-LS_239_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-08-28T18:21:10.094264+00:00",
"file_format": "fastq",
"file_size": 120816416,
"href": "/sequence-files/IGVFFI2472BMSD/@@download/IGVFFI2472BMSD.fastq.gz",
"s3_uri": "s3://igvf-files/2023/08/28/4b8f5ff8-7efd-4668-8b29-d4b1d901e9eb/IGVFFI2472BMSD.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-158_L2_SS-PKR-130_SS-V1-LEFT-HALF_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4385PBLT/",
"accession": "IGVFFI4385PBLT",
"aliases": [
"bradley-bernstein:SS-LS_2033_R2",
"bradley-bernstein:SS-LS_239_R2",
"buenrostro-bernstein:SS-LS_2033_R2",
"buenrostro-bernstein:SS-LS_239_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-08-28T18:21:11.458839+00:00",
"file_format": "fastq",
"file_size": 212224089,
"href": "/sequence-files/IGVFFI4385PBLT/@@download/IGVFFI4385PBLT.fastq.gz",
"s3_uri": "s3://igvf-files/2023/08/28/97601bee-e2ed-46b4-b0b5-4136e35e0c61/IGVFFI4385PBLT.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-158_L2_SS-PKR-130_SS-V1-LEFT-HALF_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI9756RDEZ/",
"accession": "IGVFFI9756RDEZ",
"aliases": [
"bradley-bernstein:SS-LS_2005_seqspec"
],
"content_type": "seqspec",
"creation_timestamp": "2024-09-17T22:49:55.860478+00:00",
"file_format": "yaml",
"file_size": 1186,
"href": "/configuration-files/IGVFFI9756RDEZ/@@download/IGVFFI9756RDEZ.yaml.gz",
"s3_uri": "s3://igvf-files/2024/09/17/51863c3f-d495-4582-acb5-5bc8a9288e53/IGVFFI9756RDEZ.yaml.gz",
"status": "released",
"submitted_file_name": "gs://sw-igvf-submission/seqspec-v3/SS-LS_2005_seqspecv3.yaml.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI3943XKRN/",
"accession": "IGVFFI3943XKRN",
"aliases": [
"bradley-bernstein:SS-LS_2033_seqspec"
],
"content_type": "seqspec",
"creation_timestamp": "2024-09-17T22:49:49.204467+00:00",
"file_format": "yaml",
"file_size": 1188,
"href": "/configuration-files/IGVFFI3943XKRN/@@download/IGVFFI3943XKRN.yaml.gz",
"s3_uri": "s3://igvf-files/2024/09/17/58b5ac46-4ac0-4701-80a6-dde72948ab72/IGVFFI3943XKRN.yaml.gz",
"status": "released",
"submitted_file_name": "gs://sw-igvf-submission/seqspec-v3/SS-LS_2033_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": "product",
"preferred_assay_title": "SHARE-seq",
"protocols": [
"https://www.protocols.io/view/share-seq-protocol-v2-2-di3y4gpw"
],
"related_multiome_datasets": [
{
"@id": "/measurement-sets/IGVFDS8556WPGM/",
"accession": "IGVFDS8556WPGM",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS9693BTRP/",
"accession": "IGVFDS9693BTRP",
"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": "2025-03-28T21:18:47.463115+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": "25",
"status": "released",
"submitted_by": {
"@id": "/users/c0838247-5022-46cf-a8fa-426e73bf4c94/",
"title": "Siddarth Wekhande"
},
"submitted_files_timestamp": "2023-08-28T18:21:06.450333+00:00",
"summary": "single-cell ATAC-seq (SHARE-seq)",
"uuid": "fec43dfa-d933-4eac-b4cc-2f0a8b5c604d"
}