{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS9209XACN/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS9209XACN",
"aliases": [
"buenrostro-bernstein:surya-mouse-colon_mm-set27"
],
"assay_term": {
"@id": "/assay-terms/OBI_0002764/",
"assay_slims": [
"chromatin accessibility"
],
"status": "released",
"term_name": "single-cell ATAC-seq"
},
"audit": {
"ERROR": [
{
"category": "upload status not validated",
"detail": "Sequence file [IGVFFI0879NPUS](/sequence-files/IGVFFI0879NPUS/) has `upload_status` pending. Files are expected to be validated or validation exempted.",
"level": 60,
"level_name": "ERROR",
"name": "audit_upload_status",
"path": "/sequence-files/IGVFFI0879NPUS/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS9209XACN](/measurement-sets/IGVFDS9209XACN/) has sequence file(s): [IGVFFI4354ROOZ](/sequence-files/IGVFFI4354ROOZ/), [IGVFFI1350CWOS](/sequence-files/IGVFFI1350CWOS/), [IGVFFI0879NPUS](/sequence-files/IGVFFI0879NPUS/) 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/IGVFDS9209XACN/"
},
{
"category": "missing barcode onlist",
"detail": "Measurement set [IGVFDS9209XACN](/measurement-sets/IGVFDS9209XACN/) has an `assay_term` of single-cell ATAC-seq 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/IGVFDS9209XACN/"
}
],
"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": "2025-02-07T02:06:11.838896+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/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/IGVFDO7909DHIA/",
"accession": "IGVFDO7909DHIA",
"aliases": [
"buenrostro-bernstein:surya-APC01-A1-11B"
],
"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"
},
{
"@id": "/rodent-donors/IGVFDO8555YQES/",
"accession": "IGVFDO8555YQES",
"aliases": [
"buenrostro-bernstein:surya-APC01-A1-13B"
],
"sex": "unspecified",
"status": "preview",
"taxa": "Mus musculus"
}
],
"externally_hosted": false,
"file_set_type": "experimental data",
"files": [
{
"@id": "/sequence-files/IGVFFI4354ROOZ/",
"accession": "IGVFFI4354ROOZ",
"aliases": [
"buenrostro-bernstein:surya-APC-SHARE-02-more2-ATAC.R2.fastq.gz"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-02-07T02:10:19.847463+00:00",
"file_format": "fastq",
"file_size": 19688349152,
"href": "/sequence-files/IGVFFI4354ROOZ/@@download/IGVFFI4354ROOZ.fastq.gz",
"s3_uri": "s3://igvf-files/2025/02/07/e22902ae-cedd-4332-9708-98ef56f8a433/IGVFFI4354ROOZ.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-more2-ATAC.R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1350CWOS/",
"accession": "IGVFFI1350CWOS",
"aliases": [
"buenrostro-bernstein:surya-APC-SHARE-02-more2-ATAC.R1.fastq.gz"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-02-07T02:10:07.835868+00:00",
"file_format": "fastq",
"file_size": 19671410637,
"href": "/sequence-files/IGVFFI1350CWOS/@@download/IGVFFI1350CWOS.fastq.gz",
"s3_uri": "s3://igvf-files/2025/02/07/3f16981c-9018-4266-a504-181c475e009e/IGVFFI1350CWOS.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-more2-ATAC.R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0879NPUS/",
"accession": "IGVFFI0879NPUS",
"aliases": [
"buenrostro-bernstein:surya-APC-SHARE-02-more2-ATAC.barcode.fastq.gz"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-14T15:49:09.206302+00:00",
"file_format": "fastq",
"href": "/sequence-files/IGVFFI0879NPUS/@@download/IGVFFI0879NPUS.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/14/4f1dc85a-76f1-43a3-952c-319f57141528/IGVFFI0879NPUS.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008637/",
"status": "released",
"term_name": "Illumina NovaSeq 6000"
},
"status": "in progress",
"submitted_file_name": "gs://sw-igvf-submission/surya-mouse-colitis/submit-fqs/APC-SHARE-02-more2-ATAC.barcode.fastq.gz",
"upload_status": "pending"
}
],
"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/IGVFDS5523WWKM/",
"accession": "IGVFDS5523WWKM",
"status": "preview"
},
{
"@id": "/measurement-sets/IGVFDS6123LRGF/",
"accession": "IGVFDS6123LRGF",
"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": "2025-02-07T02:10:07.835868+00:00",
"summary": "single-cell ATAC-seq (SHARE-seq)",
"uuid": "c7572238-3744-4462-a06c-e4823dabe9d8"
}