{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS2205WNED/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS2205WNED",
"aliases": [
"maya-kasowski:Scale_scRNA"
],
"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 [IGVFDS2205WNED](/measurement-sets/IGVFDS2205WNED/) has sequence file(s): [IGVFFI8723MQQV](/sequence-files/IGVFFI8723MQQV/), [IGVFFI1367BSSS](/sequence-files/IGVFFI1367BSSS/), [IGVFFI2743MDBH](/sequence-files/IGVFFI2743MDBH/), [IGVFFI9937GHAE](/sequence-files/IGVFFI9937GHAE/) 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/IGVFDS2205WNED/"
},
{
"category": "missing strand specificity",
"detail": "Measurement set [IGVFDS2205WNED](/measurement-sets/IGVFDS2205WNED/) 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/IGVFDS2205WNED/"
},
{
"category": "missing barcode onlist",
"detail": "Measurement set [IGVFDS2205WNED](/measurement-sets/IGVFDS2205WNED/) 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/IGVFDS2205WNED/"
},
{
"category": "missing barcode map",
"detail": "Multiplexed sample [IGVFSM4500AYVD](/multiplexed-samples/IGVFSM4500AYVD/) has no `barcode_map`. Multiplexed samples that use barcodes for demultiplexing are expected to specify a barcode map.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_multiplexed_sample_no_barcode_map",
"path": "/multiplexed-samples/IGVFSM4500AYVD/"
}
],
"WARNING": [
{
"category": "missing analysis",
"detail": "Measurement set [IGVFDS2205WNED](/measurement-sets/IGVFDS2205WNED/) is a raw data set with files, but is not listed in any `input_file_sets` for any analysis sets. Raw data sets with files are expected to be associated with at least one analysis set.",
"level": 40,
"level_name": "WARNING",
"name": "audit_input_for",
"path": "/measurement-sets/IGVFDS2205WNED/"
}
]
},
"award": {
"@id": "/awards/HG012076/",
"component": "mapping",
"contact_pi": {
"@id": "/users/eae4c275-1e07-45e4-ae67-3e437a8680bb/",
"title": "Ansuman Satpathy"
},
"title": "Single-cell Mapping Center for Human Regulatory Elements and Gene Activity"
},
"control_for": [],
"controlled_access": true,
"creation_timestamp": "2025-03-07T07:16:42.871494+00:00",
"data_use_limitation_summaries": [
"GRU"
],
"donors": [
{
"@id": "/human-donors/IGVFDO1129QRIW/",
"accession": "IGVFDO1129QRIW",
"aliases": [
"maya-kasowski:donor_4371"
],
"sex": "male",
"status": "released",
"taxa": "Homo sapiens"
},
{
"@id": "/human-donors/IGVFDO6383SRAQ/",
"accession": "IGVFDO6383SRAQ",
"aliases": [
"maya-kasowski:donor_4065"
],
"sex": "male",
"status": "released",
"taxa": "Homo sapiens"
},
{
"@id": "/human-donors/IGVFDO3006RCEY/",
"accession": "IGVFDO3006RCEY",
"aliases": [
"maya-kasowski:donor_4271"
],
"sex": "unspecified",
"status": "released",
"taxa": "Homo sapiens"
},
{
"@id": "/human-donors/IGVFDO4084QBKB/",
"accession": "IGVFDO4084QBKB",
"aliases": [
"maya-kasowski:donor_4522"
],
"sex": "male",
"status": "released",
"taxa": "Homo sapiens"
},
{
"@id": "/human-donors/IGVFDO7396NRBT/",
"accession": "IGVFDO7396NRBT",
"aliases": [
"maya-kasowski:donor_4102"
],
"sex": "unspecified",
"status": "released",
"taxa": "Homo sapiens"
},
{
"@id": "/human-donors/IGVFDO6768UXWX/",
"accession": "IGVFDO6768UXWX",
"aliases": [
"maya-kasowski:donor_4260"
],
"sex": "unspecified",
"status": "released",
"taxa": "Homo sapiens"
},
{
"@id": "/human-donors/IGVFDO3127CQWI/",
"accession": "IGVFDO3127CQWI",
"aliases": [
"maya-kasowski:donor_4146"
],
"sex": "female",
"status": "released",
"taxa": "Homo sapiens"
},
{
"@id": "/human-donors/IGVFDO9663VUZC/",
"accession": "IGVFDO9663VUZC",
"aliases": [
"maya-kasowski:donor_4232"
],
"sex": "unspecified",
"status": "released",
"taxa": "Homo sapiens"
},
{
"@id": "/human-donors/IGVFDO4822HOJJ/",
"accession": "IGVFDO4822HOJJ",
"aliases": [
"maya-kasowski:donor_4395"
],
"sex": "female",
"status": "released",
"taxa": "Homo sapiens"
},
{
"@id": "/human-donors/IGVFDO3656DWZS/",
"accession": "IGVFDO3656DWZS",
"aliases": [
"maya-kasowski:donor_4080"
],
"sex": "female",
"status": "released",
"taxa": "Homo sapiens"
},
{
"@id": "/human-donors/IGVFDO8056NEJH/",
"accession": "IGVFDO8056NEJH",
"aliases": [
"maya-kasowski:donor_4241"
],
"sex": "unspecified",
"status": "released",
"taxa": "Homo sapiens"
},
{
"@id": "/human-donors/IGVFDO3010QRAU/",
"accession": "IGVFDO3010QRAU",
"aliases": [
"maya-kasowski:donor_4111"
],
"sex": "female",
"status": "released",
"taxa": "Homo sapiens"
},
{
"@id": "/human-donors/IGVFDO0898EWTR/",
"accession": "IGVFDO0898EWTR",
"aliases": [
"maya-kasowski:donor_4238"
],
"sex": "male",
"status": "released",
"taxa": "Homo sapiens"
},
{
"@id": "/human-donors/IGVFDO2417NVHU/",
"accession": "IGVFDO2417NVHU",
"aliases": [
"maya-kasowski:donor_4352"
],
"sex": "female",
"status": "released",
"taxa": "Homo sapiens"
},
{
"@id": "/human-donors/IGVFDO1836DUYP/",
"accession": "IGVFDO1836DUYP",
"aliases": [
"maya-kasowski:donor_4089"
],
"sex": "unspecified",
"status": "released",
"taxa": "Homo sapiens"
},
{
"@id": "/human-donors/IGVFDO9247BXQA/",
"accession": "IGVFDO9247BXQA",
"aliases": [
"maya-kasowski:donor_4203"
],
"sex": "female",
"status": "released",
"taxa": "Homo sapiens"
},
{
"@id": "/human-donors/IGVFDO9713CSCX/",
"accession": "IGVFDO9713CSCX",
"aliases": [
"maya-kasowski:donor_4281"
],
"sex": "female",
"status": "released",
"taxa": "Homo sapiens"
},
{
"@id": "/human-donors/IGVFDO0903GCXW/",
"accession": "IGVFDO0903GCXW",
"aliases": [
"maya-kasowski:donor_4463"
],
"sex": "female",
"status": "released",
"taxa": "Homo sapiens"
},
{
"@id": "/human-donors/IGVFDO2788XNBM/",
"accession": "IGVFDO2788XNBM",
"aliases": [
"maya-kasowski:donor_4048"
],
"sex": "unspecified",
"status": "released",
"taxa": "Homo sapiens"
},
{
"@id": "/human-donors/IGVFDO9046WFVW/",
"accession": "IGVFDO9046WFVW",
"aliases": [
"maya-kasowski:donor_4262"
],
"sex": "male",
"status": "released",
"taxa": "Homo sapiens"
},
{
"@id": "/human-donors/IGVFDO5779BART/",
"accession": "IGVFDO5779BART",
"aliases": [
"maya-kasowski:donor_4535"
],
"sex": "male",
"status": "released",
"taxa": "Homo sapiens"
},
{
"@id": "/human-donors/IGVFDO9834PLUM/",
"accession": "IGVFDO9834PLUM",
"aliases": [
"maya-kasowski:donor_4268"
],
"sex": "female",
"status": "released",
"taxa": "Homo sapiens"
},
{
"@id": "/human-donors/IGVFDO9084ROFI/",
"accession": "IGVFDO9084ROFI",
"aliases": [
"maya-kasowski:donor_4066"
],
"sex": "female",
"status": "released",
"taxa": "Homo sapiens"
}
],
"externally_hosted": false,
"file_set_type": "experimental data",
"files": [
{
"@id": "/sequence-files/IGVFFI8723MQQV/",
"accession": "IGVFFI8723MQQV",
"aliases": [
"maya-kasowski:Scale_scRNA_L7_1"
],
"content_type": "reads",
"controlled_access": true,
"creation_timestamp": "2025-03-07T09:22:22.411182+00:00",
"file_format": "fastq",
"file_size": 60081362579,
"href": "/sequence-files/IGVFFI8723MQQV/@@download/IGVFFI8723MQQV.fastq.gz",
"s3_uri": "s3://igvf-restricted-files/2025/03/07/a9d90128-dd93-47cd-a75a-088f452a49cd/IGVFFI8723MQQV.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022841/",
"status": "released",
"term_name": "Illumina NovaSeq X Plus"
},
"status": "preview",
"submitted_file_name": "/users/shouvikm/data/Scale/SCALE_RNA/Scale_RNA_96/usftp21.novogene.com/01.RawData/Scale_RNA_96/Scale_RNA_96_CKDL230018055-1A_225KM5LT3_L7_1.fq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1367BSSS/",
"accession": "IGVFFI1367BSSS",
"aliases": [
"maya-kasowski:Scale_scRNA_L7_2"
],
"content_type": "reads",
"controlled_access": true,
"creation_timestamp": "2025-03-07T19:55:08.625909+00:00",
"file_format": "fastq",
"file_size": 54315881847,
"href": "/sequence-files/IGVFFI1367BSSS/@@download/IGVFFI1367BSSS.fastq.gz",
"s3_uri": "s3://igvf-restricted-files/2025/03/07/61a722d8-dfd8-4409-8291-b1caa763c2da/IGVFFI1367BSSS.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022841/",
"status": "released",
"term_name": "Illumina NovaSeq X Plus"
},
"status": "preview",
"submitted_file_name": "/users/shouvikm/data/Scale/SCALE_RNA/Scale_RNA_96/usftp21.novogene.com/01.RawData/Scale_RNA_96/Scale_RNA_96_CKDL230018055-1A_225KM5LT3_L7_2.fq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2743MDBH/",
"accession": "IGVFFI2743MDBH",
"aliases": [
"maya-kasowski:Scale_scRNA_L8_1"
],
"content_type": "reads",
"controlled_access": true,
"creation_timestamp": "2025-03-07T20:08:48.013521+00:00",
"file_format": "fastq",
"file_size": 57277418465,
"href": "/sequence-files/IGVFFI2743MDBH/@@download/IGVFFI2743MDBH.fastq.gz",
"s3_uri": "s3://igvf-restricted-files/2025/03/07/e050db70-6982-40aa-8173-a4cf8361aaac/IGVFFI2743MDBH.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022841/",
"status": "released",
"term_name": "Illumina NovaSeq X Plus"
},
"status": "preview",
"submitted_file_name": "/users/shouvikm/data/Scale/SCALE_RNA/Scale_RNA_96/usftp21.novogene.com/01.RawData/Scale_RNA_96/Scale_RNA_96_CKDL230018055-1A_225KM5LT3_L8_1.fq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9937GHAE/",
"accession": "IGVFFI9937GHAE",
"aliases": [
"maya-kasowski:Scale_scRNA_L8_2"
],
"content_type": "reads",
"controlled_access": true,
"creation_timestamp": "2025-03-07T20:23:06.404344+00:00",
"file_format": "fastq",
"file_size": 52008875168,
"href": "/sequence-files/IGVFFI9937GHAE/@@download/IGVFFI9937GHAE.fastq.gz",
"s3_uri": "s3://igvf-restricted-files/2025/03/07/f09f6627-6c25-4a88-9d14-4d28e98e8620/IGVFFI9937GHAE.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022841/",
"status": "released",
"term_name": "Illumina NovaSeq X Plus"
},
"status": "preview",
"submitted_file_name": "/users/shouvikm/data/Scale/SCALE_RNA/Scale_RNA_96/usftp21.novogene.com/01.RawData/Scale_RNA_96/Scale_RNA_96_CKDL230018055-1A_225KM5LT3_L8_2.fq.gz",
"upload_status": "validated"
}
],
"input_for": [],
"lab": {
"@id": "/labs/maya-kasowski/",
"title": "Maya Kasowski, Stanford"
},
"preferred_assay_title": "scRNA-seq",
"protocols": [
"https://www.protocols.io/view/scale-biosciences-single-cell-rna-sequencing-kit-v-x54v97e3zg3e/v1"
],
"samples": [
{
"@id": "/multiplexed-samples/IGVFSM4500AYVD/",
"@type": [
"MultiplexedSample",
"Sample",
"Item"
],
"accession": "IGVFSM4500AYVD",
"aliases": [
"maya-kasowski:multiplexed_samples_Scale_scRNA"
],
"classifications": [
"primary cell",
"multiplexed sample"
],
"disease_terms": [],
"institutional_certificates": [
{
"@id": "/institutional-certificates/5d9a7abd-9957-4b1a-91cd-72ce9610785c/",
"certificate_identifier": "IP115-20",
"controlled_access": true,
"data_use_limitation": "GRU",
"status": "released"
}
],
"modifications": [],
"sample_terms": [
{
"@id": "/sample-terms/UBERON_0002371/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"status": "released",
"summary": "bone marrow",
"term_name": "bone marrow"
}
],
"status": "preview",
"summary": "multiplexed sample: Homo sapiens bone marrow cell; Homo sapiens (female) bone marrow cell; ... and 21 more samples",
"taxa": "Homo sapiens",
"treatments": []
}
],
"schema_version": "26",
"status": "preview",
"submitted_by": {
"@id": "/users/2bebcf9d-414f-4058-8d97-00020741a419/",
"title": "Shouvik Mani"
},
"submitted_files_timestamp": "2025-03-07T09:22:22.411182+00:00",
"summary": "scRNA-seq",
"uuid": "7384ff0a-ed8b-44e3-9a99-570007dd85fa"
}