{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS8248GGOY/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS8248GGOY",
"aliases": [
"bradley-bernstein:scRNA Lib 124",
"buenrostro-bernstein:scRNA Lib 124"
],
"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 [IGVFSM9781HISX](/tissues/IGVFSM9781HISX/) 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/IGVFSM9781HISX/"
},
{
"category": "missing publication",
"detail": "Measurement set [IGVFDS8248GGOY](/measurement-sets/IGVFDS8248GGOY/) 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/IGVFDS8248GGOY/"
},
{
"category": "mismatched status",
"detail": "Released measurement set [IGVFDS8248GGOY](/measurement-sets/IGVFDS8248GGOY/) has in progress subobject tabular file [IGVFFI0400MBIM](/tabular-files/IGVFFI0400MBIM/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS8248GGOY/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing strand specificity",
"detail": "Measurement set [IGVFDS8248GGOY](/measurement-sets/IGVFDS8248GGOY/) 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/IGVFDS8248GGOY/"
}
],
"WARNING": [
{
"category": "missing age",
"detail": "Tissue [IGVFSM9781HISX](/tissues/IGVFSM9781HISX/) 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/IGVFSM9781HISX/"
}
]
},
"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": "2023-08-28T19:18:57.271657+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": [
{
"@id": "/sequence-files/IGVFFI3616NUWL/",
"accession": "IGVFFI3616NUWL",
"aliases": [
"bradley-bernstein:SS-LS_2071_R2",
"bradley-bernstein:SS-LS_256_R2",
"buenrostro-bernstein:SS-LS_2071_R2",
"buenrostro-bernstein:SS-LS_256_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-08-28T19:19:35.898295+00:00",
"file_format": "fastq",
"file_size": 791078681,
"href": "/sequence-files/IGVFFI3616NUWL/@@download/IGVFFI3616NUWL.fastq.gz",
"s3_uri": "s3://igvf-files/2023/08/28/66bd0bbd-8e9e-45e3-bb24-70250b658b2e/IGVFFI3616NUWL.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-200_L1_SS-PKR-131_SS-V1-RIGHT-HALF_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2845PDJF/",
"accession": "IGVFFI2845PDJF",
"aliases": [
"bradley-bernstein:SS-LS_2071_R1",
"bradley-bernstein:SS-LS_256_R1",
"buenrostro-bernstein:SS-LS_2071_R1",
"buenrostro-bernstein:SS-LS_256_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-08-28T19:19:34.994787+00:00",
"file_format": "fastq",
"file_size": 538324134,
"href": "/sequence-files/IGVFFI2845PDJF/@@download/IGVFFI2845PDJF.fastq.gz",
"s3_uri": "s3://igvf-files/2023/08/28/e40fef95-9d77-48e6-9c88-9274022378c1/IGVFFI2845PDJF.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-200_L1_SS-PKR-131_SS-V1-RIGHT-HALF_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5030MAFL/",
"accession": "IGVFFI5030MAFL",
"aliases": [
"bradley-bernstein:SS-LS_2118_R1",
"bradley-bernstein:SS-LS_266_R1",
"buenrostro-bernstein:SS-LS_2118_R1",
"buenrostro-bernstein:SS-LS_266_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-08-28T19:19:48.820576+00:00",
"file_format": "fastq",
"file_size": 511002164,
"href": "/sequence-files/IGVFFI5030MAFL/@@download/IGVFFI5030MAFL.fastq.gz",
"s3_uri": "s3://igvf-files/2023/08/28/4e4d4dd7-1097-479d-acee-4a63863a914e/IGVFFI5030MAFL.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-200_L2_SS-PKR-131_SS-V1-RIGHT-HALF_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5768KVWX/",
"accession": "IGVFFI5768KVWX",
"aliases": [
"bradley-bernstein:SS-LS_2118_R2",
"bradley-bernstein:SS-LS_266_R2",
"buenrostro-bernstein:SS-LS_2118_R2",
"buenrostro-bernstein:SS-LS_266_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-08-28T19:19:49.786942+00:00",
"file_format": "fastq",
"file_size": 750416637,
"href": "/sequence-files/IGVFFI5768KVWX/@@download/IGVFFI5768KVWX.fastq.gz",
"s3_uri": "s3://igvf-files/2023/08/28/5e5c27dd-c739-44d4-b8cd-5138de79bb00/IGVFFI5768KVWX.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-200_L2_SS-PKR-131_SS-V1-RIGHT-HALF_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI6115SUSK/",
"accession": "IGVFFI6115SUSK",
"aliases": [
"buenrostro-bernstein:SS-LS_2118_seqspec"
],
"content_type": "seqspec",
"creation_timestamp": "2024-09-17T22:50:26.979067+00:00",
"file_format": "yaml",
"file_size": 1228,
"href": "/configuration-files/IGVFFI6115SUSK/@@download/IGVFFI6115SUSK.yaml.gz",
"s3_uri": "s3://igvf-files/2024/09/17/4bfda42a-6ac5-4624-bf51-9f7e85ffb319/IGVFFI6115SUSK.yaml.gz",
"status": "released",
"submitted_file_name": "gs://sw-igvf-submission/seqspec-v3/SS-LS_2118_seqspecv3.yaml.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI0182TGVL/",
"accession": "IGVFFI0182TGVL",
"aliases": [
"buenrostro-bernstein:SS-LS_2071_seqspec"
],
"content_type": "seqspec",
"creation_timestamp": "2024-09-17T22:50:34.350878+00:00",
"file_format": "yaml",
"file_size": 1230,
"href": "/configuration-files/IGVFFI0182TGVL/@@download/IGVFFI0182TGVL.yaml.gz",
"s3_uri": "s3://igvf-files/2024/09/17/01a67fec-af6b-4b06-98aa-828cc97849d9/IGVFFI0182TGVL.yaml.gz",
"status": "released",
"submitted_file_name": "gs://sw-igvf-submission/seqspec-v3/SS-LS_2071_seqspecv3.yaml.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS4147RERW/"
],
"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/IGVFDS8528TQHC/",
"accession": "IGVFDS8528TQHC",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS0956TMWA/",
"accession": "IGVFDS0956TMWA",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS7709QUBW/",
"accession": "IGVFDS7709QUBW",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS8645IDXO/",
"accession": "IGVFDS8645IDXO",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS4464LQXA/",
"accession": "IGVFDS4464LQXA",
"status": "released"
}
],
"release_timestamp": "2025-03-28T21:22:25.613014+00:00",
"samples": [
{
"@id": "/tissues/IGVFSM9781HISX/",
"@type": [
"Tissue",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM9781HISX",
"aliases": [
"bradley-bernstein:BioSam 4561_SS-PKR 131",
"buenrostro-bernstein:BioSam 4561_SS-PKR 131"
],
"cellular_sub_pool": "SS-PKR 131",
"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 131)",
"taxa": "Mus musculus"
}
],
"schema_version": "26",
"status": "released",
"submitted_by": {
"@id": "/users/c0838247-5022-46cf-a8fa-426e73bf4c94/",
"title": "Siddarth Wekhande"
},
"submitted_files_timestamp": "2023-08-28T19:19:34.994787+00:00",
"summary": "single-cell RNA sequencing assay (SHARE-seq)",
"uuid": "bd6d12b1-ae9f-4805-881a-098863979540"
}