{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS8700PWZJ/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS8700PWZJ",
"aliases": [
"bradley-bernstein:scATAC Lib 120",
"buenrostro-bernstein:scATAC Lib 120"
],
"assay_term": {
"@id": "/assay-terms/OBI_0002764/",
"assay_slims": [
"chromatin accessibility"
],
"status": "released",
"term_name": "single-cell ATAC-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": "Measurement set [IGVFDS8700PWZJ](/measurement-sets/IGVFDS8700PWZJ/) 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/IGVFDS8700PWZJ/"
},
{
"category": "mismatched status",
"detail": "Released measurement set [IGVFDS8700PWZJ](/measurement-sets/IGVFDS8700PWZJ/) has in progress subobject tabular file [IGVFFI0400MBIM](/tabular-files/IGVFFI0400MBIM/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS8700PWZJ/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing strand specificity",
"detail": "Measurement set [IGVFDS8700PWZJ](/measurement-sets/IGVFDS8700PWZJ/) is missing required `strand_specificity`. Single-cell assays are expected to specify strand specificity.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_missing_strand_specificity",
"path": "/measurement-sets/IGVFDS8700PWZJ/"
}
],
"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": "2023-08-28T19:09:57.865806+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/IGVFFI7385RIWV/",
"accession": "IGVFFI7385RIWV",
"aliases": [
"bradley-bernstein:SS-LS_2056_R2",
"bradley-bernstein:SS-LS_252_R2",
"buenrostro-bernstein:SS-LS_2056_R2",
"buenrostro-bernstein:SS-LS_252_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-08-28T19:11:33.038134+00:00",
"file_format": "fastq",
"file_size": 2010557240,
"href": "/sequence-files/IGVFFI7385RIWV/@@download/IGVFFI7385RIWV.fastq.gz",
"md5sum": "9e33c9a32e566408798f6077df75e51d",
"s3_uri": "s3://igvf-files/2023/08/28/ad18e78a-b535-4c93-846e-89338b0ceb56/IGVFFI7385RIWV.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-185_L1_SS-PKR-132_2022-APRIL-R1-PLATE2-ENTIRE-PLATE_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0086MOYB/",
"accession": "IGVFFI0086MOYB",
"aliases": [
"bradley-bernstein:SS-LS_2103_R1",
"bradley-bernstein:SS-LS_262_R1",
"buenrostro-bernstein:SS-LS_2103_R1",
"buenrostro-bernstein:SS-LS_262_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-08-28T19:11:33.944629+00:00",
"file_format": "fastq",
"file_size": 1126356469,
"href": "/sequence-files/IGVFFI0086MOYB/@@download/IGVFFI0086MOYB.fastq.gz",
"md5sum": "4e96e384611344fd4309d9dfea1cb4e9",
"s3_uri": "s3://igvf-files/2023/08/28/ca2fb9eb-df6c-4196-9854-e9d7faa2726b/IGVFFI0086MOYB.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-185_L2_SS-PKR-132_2022-APRIL-R1-PLATE2-ENTIRE-PLATE_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0043UUDP/",
"accession": "IGVFFI0043UUDP",
"aliases": [
"bradley-bernstein:SS-LS_2103_R2",
"bradley-bernstein:SS-LS_262_R2",
"buenrostro-bernstein:SS-LS_2103_R2",
"buenrostro-bernstein:SS-LS_262_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-08-28T19:11:34.810435+00:00",
"file_format": "fastq",
"file_size": 2009121908,
"href": "/sequence-files/IGVFFI0043UUDP/@@download/IGVFFI0043UUDP.fastq.gz",
"md5sum": "32953d7f2548254e4b0c77e3b7514834",
"s3_uri": "s3://igvf-files/2023/08/28/5c23ded9-fafb-4c16-b845-141bd1ec17a9/IGVFFI0043UUDP.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-185_L2_SS-PKR-132_2022-APRIL-R1-PLATE2-ENTIRE-PLATE_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7270DMRN/",
"accession": "IGVFFI7270DMRN",
"aliases": [
"bradley-bernstein:SS-LS_2056_R1",
"bradley-bernstein:SS-LS_252_R1",
"buenrostro-bernstein:SS-LS_2056_R1",
"buenrostro-bernstein:SS-LS_252_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-08-28T19:11:32.113365+00:00",
"file_format": "fastq",
"file_size": 1125139265,
"href": "/sequence-files/IGVFFI7270DMRN/@@download/IGVFFI7270DMRN.fastq.gz",
"md5sum": "d20622c9546f8e063fd4343a64dc75d1",
"s3_uri": "s3://igvf-files/2023/08/28/fed67581-b461-45ae-b768-71174b5392bf/IGVFFI7270DMRN.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-185_L1_SS-PKR-132_2022-APRIL-R1-PLATE2-ENTIRE-PLATE_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI6768ERPY/",
"accession": "IGVFFI6768ERPY",
"aliases": [
"bradley-bernstein:SS-LS_2103_seqspec"
],
"content_type": "seqspec",
"creation_timestamp": "2024-09-17T22:49:38.046963+00:00",
"file_format": "yaml",
"file_size": 1188,
"href": "/configuration-files/IGVFFI6768ERPY/@@download/IGVFFI6768ERPY.yaml.gz",
"md5sum": "b7e4e4e3cb324708de6cf548dc4757fc",
"s3_uri": "s3://igvf-files/2024/09/17/b43035cc-ba33-4c29-813a-64bb3a32d2bc/IGVFFI6768ERPY.yaml.gz",
"status": "released",
"submitted_file_name": "gs://sw-igvf-submission/seqspec-v3/SS-LS_2103_seqspecv3.yaml.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI0846TMYA/",
"accession": "IGVFFI0846TMYA",
"aliases": [
"bradley-bernstein:SS-LS_2056_seqspec"
],
"content_type": "seqspec",
"creation_timestamp": "2024-09-17T22:49:44.972781+00:00",
"file_format": "yaml",
"file_size": 1189,
"href": "/configuration-files/IGVFFI0846TMYA/@@download/IGVFFI0846TMYA.yaml.gz",
"md5sum": "06228e39befd395efddfee3c64ea1fd3",
"s3_uri": "s3://igvf-files/2024/09/17/67546b9a-3de9-4e40-b159-a455cf587cd8/IGVFFI0846TMYA.yaml.gz",
"status": "released",
"submitted_file_name": "gs://sw-igvf-submission/seqspec-v3/SS-LS_2056_seqspecv3.yaml.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS4769QTGM/"
],
"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/IGVFDS9620KXMW/",
"accession": "IGVFDS9620KXMW",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS9728TWXO/",
"accession": "IGVFDS9728TWXO",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS6721DTCZ/",
"accession": "IGVFDS6721DTCZ",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS7747XDUI/",
"accession": "IGVFDS7747XDUI",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS4161OUYL/",
"accession": "IGVFDS4161OUYL",
"status": "released"
}
],
"release_timestamp": "2025-03-28T21:22:50.092919+00:00",
"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": "26",
"status": "released",
"submitted_by": {
"@id": "/users/c0838247-5022-46cf-a8fa-426e73bf4c94/",
"title": "Siddarth Wekhande"
},
"submitted_files_timestamp": "2023-08-28T19:11:32.113365+00:00",
"summary": "single-cell ATAC-seq (SHARE-seq)",
"uuid": "72439d6a-db66-446a-8f7c-093909cbff6d"
}