{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS5523WWKM/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS5523WWKM",
"aliases": [
"buenrostro-bernstein:surya-mouse-colon_mm-set28"
],
"assay_term": {
"@id": "/assay-terms/OBI_0002631/",
"assay_slims": [
"gene expression"
],
"status": "released",
"term_name": "single-cell RNA sequencing assay"
},
"audit": {
"NOT_COMPLIANT": [
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS5523WWKM](/measurement-sets/IGVFDS5523WWKM/) has sequence file(s): [IGVFFI2447KHFY](/sequence-files/IGVFFI2447KHFY/), [IGVFFI8022FSUK](/sequence-files/IGVFFI8022FSUK/) which do not have any `seqspecs`. Sequence files in a file set associated with single cell data are expected to link to a sequence specification file.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_missing_seqspec",
"path": "/measurement-sets/IGVFDS5523WWKM/"
},
{
"category": "missing barcode onlist",
"detail": "Measurement set [IGVFDS5523WWKM](/measurement-sets/IGVFDS5523WWKM/) has an `assay_term` of single-cell RNA sequencing assay but no `onlist_files` nor `onlist_methods`. Measurement sets to be processed via the single cell uniform pipeline are expected to have onlist files and onlist methods indicated.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_onlist",
"path": "/measurement-sets/IGVFDS5523WWKM/"
}
],
"WARNING": [
{
"category": "missing age",
"detail": "Tissue [IGVFSM6844DNNZ](/tissues/IGVFSM6844DNNZ/) 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/IGVFSM6844DNNZ/"
}
]
},
"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": "2025-02-07T02:06:12.789200+00:00",
"description": "Colitis_recovered_adenoma APC01-A1-7B,APC01-B1-4B; Control_adenoma APC01-A1-11B,APC01-A1-13B,APC01-B1-6B",
"donors": [
{
"@id": "/rodent-donors/IGVFDO8555YQES/",
"accession": "IGVFDO8555YQES",
"aliases": [
"buenrostro-bernstein:surya-APC01-A1-13B"
],
"sex": "unspecified",
"status": "preview",
"taxa": "Mus musculus"
},
{
"@id": "/rodent-donors/IGVFDO7909DHIA/",
"accession": "IGVFDO7909DHIA",
"aliases": [
"buenrostro-bernstein:surya-APC01-A1-11B"
],
"sex": "unspecified",
"status": "preview",
"taxa": "Mus musculus"
},
{
"@id": "/rodent-donors/IGVFDO0418WVMT/",
"accession": "IGVFDO0418WVMT",
"aliases": [
"buenrostro-bernstein:surya-APC01-B1-6B"
],
"sex": "unspecified",
"status": "preview",
"taxa": "Mus musculus"
},
{
"@id": "/rodent-donors/IGVFDO1366PENC/",
"accession": "IGVFDO1366PENC",
"aliases": [
"buenrostro-bernstein:surya-APC01-B1-4B"
],
"sex": "unspecified",
"status": "preview",
"taxa": "Mus musculus"
},
{
"@id": "/rodent-donors/IGVFDO6621DZIL/",
"accession": "IGVFDO6621DZIL",
"aliases": [
"buenrostro-bernstein:surya-APC01-A1-7B"
],
"sex": "unspecified",
"status": "preview",
"taxa": "Mus musculus"
}
],
"externally_hosted": false,
"file_set_type": "experimental data",
"files": [
{
"@id": "/sequence-files/IGVFFI2447KHFY/",
"accession": "IGVFFI2447KHFY",
"aliases": [
"buenrostro-bernstein:surya-APC-SHARE-02-5k-RNA.R1.fastq.gz"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-02-07T02:10:09.982078+00:00",
"file_format": "fastq",
"file_size": 2994646030,
"href": "/sequence-files/IGVFFI2447KHFY/@@download/IGVFFI2447KHFY.fastq.gz",
"s3_uri": "s3://igvf-files/2025/02/07/b7fe90d8-9a96-49b0-9334-9df95174d996/IGVFFI2447KHFY.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008637/",
"status": "released",
"term_name": "Illumina NovaSeq 6000"
},
"status": "preview",
"submitted_file_name": "gs://sw-igvf-submission/surya-mouse-colitis/submit-fqs/APC-SHARE-02-5k-RNA.R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8022FSUK/",
"accession": "IGVFFI8022FSUK",
"aliases": [
"buenrostro-bernstein:surya-APC-SHARE-02-5k-RNA.R2.fastq.gz"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-02-07T02:10:22.260697+00:00",
"file_format": "fastq",
"file_size": 3472628093,
"href": "/sequence-files/IGVFFI8022FSUK/@@download/IGVFFI8022FSUK.fastq.gz",
"s3_uri": "s3://igvf-files/2025/02/07/f3bcc5fc-1a77-41ec-b104-2856260a90d3/IGVFFI8022FSUK.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008637/",
"status": "released",
"term_name": "Illumina NovaSeq 6000"
},
"status": "preview",
"submitted_file_name": "gs://sw-igvf-submission/surya-mouse-colitis/submit-fqs/APC-SHARE-02-5k-RNA.R2.fastq.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS5153IDEO/"
],
"lab": {
"@id": "/labs/jason-buenrostro/",
"title": "Jason Buenrostro, Broad"
},
"multiome_size": 5,
"preferred_assay_title": "SHARE-seq",
"protocols": [
"https://www.protocols.io/view/share-seq-v1-6qpvrdexpgmk/v1"
],
"related_multiome_datasets": [
{
"@id": "/measurement-sets/IGVFDS4128FOHH/",
"accession": "IGVFDS4128FOHH",
"status": "preview"
},
{
"@id": "/measurement-sets/IGVFDS3977RUCK/",
"accession": "IGVFDS3977RUCK",
"status": "preview"
},
{
"@id": "/measurement-sets/IGVFDS6123LRGF/",
"accession": "IGVFDS6123LRGF",
"status": "preview"
},
{
"@id": "/measurement-sets/IGVFDS9209XACN/",
"accession": "IGVFDS9209XACN",
"status": "preview"
}
],
"samples": [
{
"@id": "/tissues/IGVFSM6844DNNZ/",
"@type": [
"Tissue",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM6844DNNZ",
"aliases": [
"buenrostro-bernstein:surya-APC01-A1-7B,APC01-B1-4B,APC01-A1-11B,APC01-A1-13B,APC01-B1-6B"
],
"classifications": [
"tissue"
],
"institutional_certificates": [],
"sample_terms": [
{
"@id": "/sample-terms/UBERON_0001155/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"status": "released",
"summary": "colon",
"term_name": "colon"
}
],
"status": "preview",
"summary": "colon tissue, Mus musculus C57BL/6J",
"taxa": "Mus musculus"
}
],
"schema_version": "25",
"status": "preview",
"submitted_by": {
"@id": "/users/c0838247-5022-46cf-a8fa-426e73bf4c94/",
"title": "Siddarth Wekhande"
},
"submitted_files_timestamp": "2025-02-07T02:10:09.982078+00:00",
"summary": "single-cell RNA sequencing assay (SHARE-seq)",
"uuid": "fd21fce2-8310-4a1a-9472-9825194b9529"
}