{
"@context": "/terms/",
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"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS4128FOHH",
"aliases": [
"buenrostro-bernstein:surya-mouse-colon_mm-set26"
],
"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 [IGVFSM6844DNNZ](/tissues/IGVFSM6844DNNZ/) 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/IGVFSM6844DNNZ/"
},
{
"category": "missing publication",
"detail": "Measurement set [IGVFDS4128FOHH](/measurement-sets/IGVFDS4128FOHH/) 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/IGVFDS4128FOHH/"
}
],
"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": "2025-02-07T02:06:10.618193+00:00",
"data_use_limitation_summaries": [
"no certificate"
],
"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/IGVFDO1366PENC/",
"accession": "IGVFDO1366PENC",
"aliases": [
"buenrostro-bernstein:surya-APC01-B1-4B"
],
"sex": "unspecified",
"status": "released",
"taxa": "Mus musculus"
},
{
"@id": "/rodent-donors/IGVFDO7909DHIA/",
"accession": "IGVFDO7909DHIA",
"aliases": [
"buenrostro-bernstein:surya-APC01-A1-11B"
],
"sex": "unspecified",
"status": "released",
"taxa": "Mus musculus"
},
{
"@id": "/rodent-donors/IGVFDO8555YQES/",
"accession": "IGVFDO8555YQES",
"aliases": [
"buenrostro-bernstein:surya-APC01-A1-13B"
],
"sex": "unspecified",
"status": "released",
"taxa": "Mus musculus"
},
{
"@id": "/rodent-donors/IGVFDO6621DZIL/",
"accession": "IGVFDO6621DZIL",
"aliases": [
"buenrostro-bernstein:surya-APC01-A1-7B"
],
"sex": "unspecified",
"status": "released",
"taxa": "Mus musculus"
},
{
"@id": "/rodent-donors/IGVFDO0418WVMT/",
"accession": "IGVFDO0418WVMT",
"aliases": [
"buenrostro-bernstein:surya-APC01-B1-6B"
],
"sex": "unspecified",
"status": "released",
"taxa": "Mus musculus"
}
],
"externally_hosted": false,
"file_set_type": "experimental data",
"files": [
{
"@id": "/configuration-files/IGVFFI2654VXSR/",
"accession": "IGVFFI2654VXSR",
"aliases": [
"buenrostro-bernstein:IGVFFI2941MMCJ_seqspec"
],
"content_type": "seqspec",
"creation_timestamp": "2025-03-18T17:54:07.049329+00:00",
"file_format": "yaml",
"file_size": 1219,
"href": "/configuration-files/IGVFFI2654VXSR/@@download/IGVFFI2654VXSR.yaml.gz",
"md5sum": "de7b47d1542e88ac1d44d81dd4334480",
"s3_uri": "s3://igvf-files/2025/03/18/92853d44-a5db-415a-bf0d-09cc927b2a1e/IGVFFI2654VXSR.yaml.gz",
"status": "released",
"submitted_file_name": "gs://sw-igvf-submission/surya-mouse-colitis/seqspecs/IGVFFI2941MMCJ_seqspec.yaml.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2941MMCJ/",
"accession": "IGVFFI2941MMCJ",
"aliases": [
"buenrostro-bernstein:surya-APC-SHARE-02-more1-ATAC.R1.fastq.gz"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-02-07T02:10:05.685322+00:00",
"file_format": "fastq",
"file_size": 6676687998,
"href": "/sequence-files/IGVFFI2941MMCJ/@@download/IGVFFI2941MMCJ.fastq.gz",
"md5sum": "fd8526c23629eca2626a1ee70b7ff0e5",
"s3_uri": "s3://igvf-files/2025/02/07/5eb9beb8-6865-4437-9b58-39785c23a0ed/IGVFFI2941MMCJ.fastq.gz",
"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NovaSeq 6000"
},
"status": "released",
"submitted_file_name": "gs://sw-igvf-submission/surya-mouse-colitis/submit-fqs/APC-SHARE-02-more1-ATAC.R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9334WAOR/",
"accession": "IGVFFI9334WAOR",
"aliases": [
"buenrostro-bernstein:surya-APC-SHARE-02-more1-ATAC.R2.fastq.gz"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-02-07T02:10:17.406314+00:00",
"file_format": "fastq",
"file_size": 6688020663,
"href": "/sequence-files/IGVFFI9334WAOR/@@download/IGVFFI9334WAOR.fastq.gz",
"md5sum": "600f952902e7dfb56146ece7c24615f8",
"s3_uri": "s3://igvf-files/2025/02/07/487db182-cecd-4f17-8848-d482cd2f4b4e/IGVFFI9334WAOR.fastq.gz",
"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NovaSeq 6000"
},
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7197NSEL/",
"accession": "IGVFFI7197NSEL",
"aliases": [
"buenrostro-bernstein:surya-APC-SHARE-02-more1-ATAC.barcode.fastq.gz"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-14T15:49:02.936816+00:00",
"file_format": "fastq",
"file_size": 2452354107,
"href": "/sequence-files/IGVFFI7197NSEL/@@download/IGVFFI7197NSEL.fastq.gz",
"md5sum": "5558b06b746e48e676b282e6336137e3",
"s3_uri": "s3://igvf-files/2025/03/14/4a87c98d-3d0e-4832-b0d9-c5719335aa27/IGVFFI7197NSEL.fastq.gz",
"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NovaSeq 6000"
},
"status": "released",
"submitted_file_name": "gs://sw-igvf-submission/surya-mouse-colitis/submit-fqs/barcode-file/APC-SHARE-02-more1-ATAC.barcode.fastq.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS5153IDEO/"
],
"lab": {
"@id": "/labs/jason-buenrostro/",
"title": "Jason Buenrostro, Broad"
},
"multiome_size": 5,
"onlist_files": [
"/tabular-files/IGVFFI4393VVCW/",
"/tabular-files/IGVFFI9683HRGJ/"
],
"onlist_method": "product",
"preferred_assay_title": "SHARE-seq",
"protocols": [
"https://www.protocols.io/view/share-seq-v1-6qpvrdexpgmk/v1"
],
"related_multiome_datasets": [
{
"@id": "/measurement-sets/IGVFDS3977RUCK/",
"accession": "IGVFDS3977RUCK",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS5523WWKM/",
"accession": "IGVFDS5523WWKM",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS6123LRGF/",
"accession": "IGVFDS6123LRGF",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS9209XACN/",
"accession": "IGVFDS9209XACN",
"status": "released"
}
],
"release_timestamp": "2025-03-26T17:33:39.964999+00:00",
"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": "released",
"summary": "Mus musculus C57BL/6J colon tissue",
"taxa": "Mus musculus"
}
],
"schema_version": "26",
"status": "released",
"submitted_by": {
"@id": "/users/c0838247-5022-46cf-a8fa-426e73bf4c94/",
"title": "Siddarth Wekhande"
},
"submitted_files_timestamp": "2025-02-07T02:10:05.685322+00:00",
"summary": "single-cell ATAC-seq (SHARE-seq)",
"uuid": "bc77cb17-8a47-460e-875d-45018784a32f"
}