{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS1790XLZR/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS1790XLZR",
"aliases": [
"maya-kasowski:Scale_scATAC"
],
"assay_term": {
"@id": "/assay-terms/OBI_0002764/",
"assay_slims": [
"chromatin accessibility"
],
"status": "released",
"term_name": "single-cell ATAC-seq"
},
"audit": {
"NOT_COMPLIANT": [
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS1790XLZR](/measurement-sets/IGVFDS1790XLZR/) has sequence file(s): [IGVFFI3045PSVF](/sequence-files/IGVFFI3045PSVF/), [IGVFFI9400PCJC](/sequence-files/IGVFFI9400PCJC/), [IGVFFI9683OGKB](/sequence-files/IGVFFI9683OGKB/), [IGVFFI7175PWFQ](/sequence-files/IGVFFI7175PWFQ/), [IGVFFI8281UNYH](/sequence-files/IGVFFI8281UNYH/), [IGVFFI6287WWQN](/sequence-files/IGVFFI6287WWQN/), [IGVFFI4367MEQN](/sequence-files/IGVFFI4367MEQN/), [IGVFFI6282BKKE](/sequence-files/IGVFFI6282BKKE/), [IGVFFI7884GSVE](/sequence-files/IGVFFI7884GSVE/), [IGVFFI2398NHKF](/sequence-files/IGVFFI2398NHKF/), [IGVFFI3960XUKA](/sequence-files/IGVFFI3960XUKA/), [IGVFFI7653OJMO](/sequence-files/IGVFFI7653OJMO/), [IGVFFI6461OIYJ](/sequence-files/IGVFFI6461OIYJ/), [IGVFFI7730PTDV](/sequence-files/IGVFFI7730PTDV/), [IGVFFI9350NWNT](/sequence-files/IGVFFI9350NWNT/), [IGVFFI3361KDGU](/sequence-files/IGVFFI3361KDGU/), [IGVFFI4003TGJY](/sequence-files/IGVFFI4003TGJY/), [IGVFFI1148TXMZ](/sequence-files/IGVFFI1148TXMZ/), [IGVFFI4919YHUQ](/sequence-files/IGVFFI4919YHUQ/), [IGVFFI4893CRTK](/sequence-files/IGVFFI4893CRTK/), [IGVFFI6964PMSI](/sequence-files/IGVFFI6964PMSI/), [IGVFFI6310TFWS](/sequence-files/IGVFFI6310TFWS/), [IGVFFI7069AMLZ](/sequence-files/IGVFFI7069AMLZ/), [IGVFFI5012UHJY](/sequence-files/IGVFFI5012UHJY/) 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/IGVFDS1790XLZR/"
},
{
"category": "missing strand specificity",
"detail": "Measurement set [IGVFDS1790XLZR](/measurement-sets/IGVFDS1790XLZR/) 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/IGVFDS1790XLZR/"
},
{
"category": "missing barcode onlist",
"detail": "Measurement set [IGVFDS1790XLZR](/measurement-sets/IGVFDS1790XLZR/) 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/IGVFDS1790XLZR/"
},
{
"category": "missing barcode map",
"detail": "Multiplexed sample [IGVFSM1625LLXE](/multiplexed-samples/IGVFSM1625LLXE/) 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/IGVFSM1625LLXE/"
}
],
"WARNING": [
{
"category": "missing analysis",
"detail": "Measurement set [IGVFDS1790XLZR](/measurement-sets/IGVFDS1790XLZR/) 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/IGVFDS1790XLZR/"
}
]
},
"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": "2025-03-07T07:16:40.229972+00:00",
"data_use_limitation_summaries": [
"GRU"
],
"donors": [
{
"@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/IGVFDO1836DUYP/",
"accession": "IGVFDO1836DUYP",
"aliases": [
"maya-kasowski:donor_4089"
],
"sex": "unspecified",
"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/IGVFDO1129QRIW/",
"accession": "IGVFDO1129QRIW",
"aliases": [
"maya-kasowski:donor_4371"
],
"sex": "male",
"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/IGVFDO9834PLUM/",
"accession": "IGVFDO9834PLUM",
"aliases": [
"maya-kasowski:donor_4268"
],
"sex": "female",
"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/IGVFDO3010QRAU/",
"accession": "IGVFDO3010QRAU",
"aliases": [
"maya-kasowski:donor_4111"
],
"sex": "female",
"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/IGVFDO4084QBKB/",
"accession": "IGVFDO4084QBKB",
"aliases": [
"maya-kasowski:donor_4522"
],
"sex": "male",
"status": "released",
"taxa": "Homo sapiens"
},
{
"@id": "/human-donors/IGVFDO9084ROFI/",
"accession": "IGVFDO9084ROFI",
"aliases": [
"maya-kasowski:donor_4066"
],
"sex": "female",
"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/IGVFDO3006RCEY/",
"accession": "IGVFDO3006RCEY",
"aliases": [
"maya-kasowski:donor_4271"
],
"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/IGVFDO4822HOJJ/",
"accession": "IGVFDO4822HOJJ",
"aliases": [
"maya-kasowski:donor_4395"
],
"sex": "female",
"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/IGVFDO9713CSCX/",
"accession": "IGVFDO9713CSCX",
"aliases": [
"maya-kasowski:donor_4281"
],
"sex": "female",
"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/IGVFDO3656DWZS/",
"accession": "IGVFDO3656DWZS",
"aliases": [
"maya-kasowski:donor_4080"
],
"sex": "female",
"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/IGVFDO7396NRBT/",
"accession": "IGVFDO7396NRBT",
"aliases": [
"maya-kasowski:donor_4102"
],
"sex": "unspecified",
"status": "released",
"taxa": "Homo sapiens"
}
],
"externally_hosted": false,
"file_set_type": "experimental data",
"files": [
{
"@id": "/sequence-files/IGVFFI3045PSVF/",
"accession": "IGVFFI3045PSVF",
"aliases": [
"maya-kasowski:Scale_scATAC_lane4_R1"
],
"content_type": "reads",
"controlled_access": true,
"creation_timestamp": "2025-03-07T22:30:11.964420+00:00",
"file_format": "fastq",
"file_size": 31462239362,
"href": "/sequence-files/IGVFFI3045PSVF/@@download/IGVFFI3045PSVF.fastq.gz",
"s3_uri": "s3://igvf-restricted-files/2025/03/07/9cfa6bb9-70b2-4dd8-af05-319f1afe8d4f/IGVFFI3045PSVF.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008637/",
"status": "released",
"term_name": "Illumina NovaSeq 6000"
},
"status": "preview",
"submitted_file_name": "/users/shouvikm/data/Scale/SCALE_leukemia_01202023/fastqs_after_scATAC_Scale_pipeline/S701-S706/S704/S704P_S4_L003_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9400PCJC/",
"accession": "IGVFFI9400PCJC",
"aliases": [
"maya-kasowski:Scale_scATAC_lane3_I1"
],
"content_type": "reads",
"controlled_access": true,
"creation_timestamp": "2025-03-07T22:01:27.317449+00:00",
"file_format": "fastq",
"file_size": 9557092740,
"href": "/sequence-files/IGVFFI9400PCJC/@@download/IGVFFI9400PCJC.fastq.gz",
"s3_uri": "s3://igvf-restricted-files/2025/03/07/46f9019d-e468-4002-86db-0d91caa7204d/IGVFFI9400PCJC.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008637/",
"status": "released",
"term_name": "Illumina NovaSeq 6000"
},
"status": "preview",
"submitted_file_name": "/users/shouvikm/data/Scale/SCALE_leukemia_01202023/fastqs_after_scATAC_Scale_pipeline/S701-S706/S703/S703P_S3_L003_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9683OGKB/",
"accession": "IGVFFI9683OGKB",
"aliases": [
"maya-kasowski:Scale_scATAC_lane5_I1"
],
"content_type": "reads",
"controlled_access": true,
"creation_timestamp": "2025-03-07T22:47:16.674104+00:00",
"file_format": "fastq",
"file_size": 10263339676,
"href": "/sequence-files/IGVFFI9683OGKB/@@download/IGVFFI9683OGKB.fastq.gz",
"s3_uri": "s3://igvf-restricted-files/2025/03/07/561a981a-cf81-42fc-bdc0-5423ad478a88/IGVFFI9683OGKB.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008637/",
"status": "released",
"term_name": "Illumina NovaSeq 6000"
},
"status": "preview",
"submitted_file_name": "/users/shouvikm/data/Scale/SCALE_leukemia_01202023/fastqs_after_scATAC_Scale_pipeline/S701-S706/S705/S705P_S5_L003_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7175PWFQ/",
"accession": "IGVFFI7175PWFQ",
"aliases": [
"maya-kasowski:Scale_scATAC_lane5_R2"
],
"content_type": "reads",
"controlled_access": true,
"creation_timestamp": "2025-03-07T23:01:38.446381+00:00",
"file_format": "fastq",
"file_size": 46693909759,
"href": "/sequence-files/IGVFFI7175PWFQ/@@download/IGVFFI7175PWFQ.fastq.gz",
"s3_uri": "s3://igvf-restricted-files/2025/03/07/0bfb22cc-915c-4c52-b0ea-e39c296ed0ee/IGVFFI7175PWFQ.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008637/",
"status": "released",
"term_name": "Illumina NovaSeq 6000"
},
"status": "preview",
"submitted_file_name": "/users/shouvikm/data/Scale/SCALE_leukemia_01202023/fastqs_after_scATAC_Scale_pipeline/S701-S706/S705/S705P_S5_L003_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8281UNYH/",
"accession": "IGVFFI8281UNYH",
"aliases": [
"maya-kasowski:Scale_scATAC_lane3_R1"
],
"content_type": "reads",
"controlled_access": true,
"creation_timestamp": "2025-03-07T22:07:32.390287+00:00",
"file_format": "fastq",
"file_size": 33548575771,
"href": "/sequence-files/IGVFFI8281UNYH/@@download/IGVFFI8281UNYH.fastq.gz",
"s3_uri": "s3://igvf-restricted-files/2025/03/07/77047be0-4848-451f-8b20-e9572aad1549/IGVFFI8281UNYH.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008637/",
"status": "released",
"term_name": "Illumina NovaSeq 6000"
},
"status": "preview",
"submitted_file_name": "/users/shouvikm/data/Scale/SCALE_leukemia_01202023/fastqs_after_scATAC_Scale_pipeline/S701-S706/S703/S703P_S3_L003_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6287WWQN/",
"accession": "IGVFFI6287WWQN",
"aliases": [
"maya-kasowski:Scale_scATAC_lane1_R2"
],
"content_type": "reads",
"controlled_access": true,
"creation_timestamp": "2025-03-07T21:01:29.164023+00:00",
"file_format": "fastq",
"file_size": 46320485581,
"href": "/sequence-files/IGVFFI6287WWQN/@@download/IGVFFI6287WWQN.fastq.gz",
"s3_uri": "s3://igvf-restricted-files/2025/03/07/49d50929-d2b3-4fba-b1e2-fb10edb28a00/IGVFFI6287WWQN.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008637/",
"status": "released",
"term_name": "Illumina NovaSeq 6000"
},
"status": "preview",
"submitted_file_name": "/users/shouvikm/data/Scale/SCALE_leukemia_01202023/fastqs_after_scATAC_Scale_pipeline/S701-S706/S701/S701P_S1_L003_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4367MEQN/",
"accession": "IGVFFI4367MEQN",
"aliases": [
"maya-kasowski:Scale_scATAC_lane1_R1"
],
"content_type": "reads",
"controlled_access": true,
"creation_timestamp": "2025-03-07T20:42:18.411939+00:00",
"file_format": "fastq",
"file_size": 36285556121,
"href": "/sequence-files/IGVFFI4367MEQN/@@download/IGVFFI4367MEQN.fastq.gz",
"s3_uri": "s3://igvf-restricted-files/2025/03/07/8f47f62a-011c-42de-bca5-bc6e71dd01de/IGVFFI4367MEQN.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008637/",
"status": "released",
"term_name": "Illumina NovaSeq 6000"
},
"status": "preview",
"submitted_file_name": "/users/shouvikm/data/Scale/SCALE_leukemia_01202023/fastqs_after_scATAC_Scale_pipeline/S701-S706/S701/S701P_S1_L003_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6282BKKE/",
"accession": "IGVFFI6282BKKE",
"aliases": [
"maya-kasowski:Scale_scATAC_lane1_I2"
],
"content_type": "reads",
"controlled_access": true,
"creation_timestamp": "2025-03-07T20:38:49.340535+00:00",
"file_format": "fastq",
"file_size": 14044663624,
"href": "/sequence-files/IGVFFI6282BKKE/@@download/IGVFFI6282BKKE.fastq.gz",
"s3_uri": "s3://igvf-restricted-files/2025/03/07/b67eae49-e3a0-4602-b749-624dc26406e1/IGVFFI6282BKKE.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008637/",
"status": "released",
"term_name": "Illumina NovaSeq 6000"
},
"status": "preview",
"submitted_file_name": "/users/shouvikm/data/Scale/SCALE_leukemia_01202023/fastqs_after_scATAC_Scale_pipeline/S701-S706/S701/S701P_S1_L003_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7884GSVE/",
"accession": "IGVFFI7884GSVE",
"aliases": [
"maya-kasowski:Scale_scATAC_lane1_I1"
],
"content_type": "reads",
"controlled_access": true,
"creation_timestamp": "2025-03-07T20:36:18.987147+00:00",
"file_format": "fastq",
"file_size": 10304855508,
"href": "/sequence-files/IGVFFI7884GSVE/@@download/IGVFFI7884GSVE.fastq.gz",
"s3_uri": "s3://igvf-restricted-files/2025/03/07/816c4cdf-93ef-499b-986a-20d2571689d0/IGVFFI7884GSVE.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008637/",
"status": "released",
"term_name": "Illumina NovaSeq 6000"
},
"status": "preview",
"submitted_file_name": "/users/shouvikm/data/Scale/SCALE_leukemia_01202023/fastqs_after_scATAC_Scale_pipeline/S701-S706/S701/S701P_S1_L003_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2398NHKF/",
"accession": "IGVFFI2398NHKF",
"aliases": [
"maya-kasowski:Scale_scATAC_lane2_I1"
],
"content_type": "reads",
"controlled_access": true,
"creation_timestamp": "2025-03-07T21:29:55.937266+00:00",
"file_format": "fastq",
"file_size": 8942534187,
"href": "/sequence-files/IGVFFI2398NHKF/@@download/IGVFFI2398NHKF.fastq.gz",
"s3_uri": "s3://igvf-restricted-files/2025/03/07/b0dd4854-db16-4759-a157-0a6f8e43be64/IGVFFI2398NHKF.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008637/",
"status": "released",
"term_name": "Illumina NovaSeq 6000"
},
"status": "preview",
"submitted_file_name": "/users/shouvikm/data/Scale/SCALE_leukemia_01202023/fastqs_after_scATAC_Scale_pipeline/S701-S706/S702/S702P_S2_L003_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3960XUKA/",
"accession": "IGVFFI3960XUKA",
"aliases": [
"maya-kasowski:Scale_scATAC_lane2_I2"
],
"content_type": "reads",
"controlled_access": true,
"creation_timestamp": "2025-03-07T21:35:21.458976+00:00",
"file_format": "fastq",
"file_size": 12134045445,
"href": "/sequence-files/IGVFFI3960XUKA/@@download/IGVFFI3960XUKA.fastq.gz",
"s3_uri": "s3://igvf-restricted-files/2025/03/07/54d97e26-49aa-4719-b1b7-0ae7dd353fb6/IGVFFI3960XUKA.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008637/",
"status": "released",
"term_name": "Illumina NovaSeq 6000"
},
"status": "preview",
"submitted_file_name": "/users/shouvikm/data/Scale/SCALE_leukemia_01202023/fastqs_after_scATAC_Scale_pipeline/S701-S706/S702/S702P_S2_L003_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7653OJMO/",
"accession": "IGVFFI7653OJMO",
"aliases": [
"maya-kasowski:Scale_scATAC_lane4_I1"
],
"content_type": "reads",
"controlled_access": true,
"creation_timestamp": "2025-03-07T22:25:14.297234+00:00",
"file_format": "fastq",
"file_size": 8804943228,
"href": "/sequence-files/IGVFFI7653OJMO/@@download/IGVFFI7653OJMO.fastq.gz",
"s3_uri": "s3://igvf-restricted-files/2025/03/07/a927278b-e81d-433b-917a-320507385527/IGVFFI7653OJMO.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008637/",
"status": "released",
"term_name": "Illumina NovaSeq 6000"
},
"status": "preview",
"submitted_file_name": "/users/shouvikm/data/Scale/SCALE_leukemia_01202023/fastqs_after_scATAC_Scale_pipeline/S701-S706/S704/S704P_S4_L003_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6461OIYJ/",
"accession": "IGVFFI6461OIYJ",
"aliases": [
"maya-kasowski:Scale_scATAC_lane5_I2"
],
"content_type": "reads",
"controlled_access": true,
"creation_timestamp": "2025-03-07T22:49:48.467860+00:00",
"file_format": "fastq",
"file_size": 14293739184,
"href": "/sequence-files/IGVFFI6461OIYJ/@@download/IGVFFI6461OIYJ.fastq.gz",
"s3_uri": "s3://igvf-restricted-files/2025/03/07/b4d7d42a-8732-4760-9482-c082d3b979c2/IGVFFI6461OIYJ.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008637/",
"status": "released",
"term_name": "Illumina NovaSeq 6000"
},
"status": "preview",
"submitted_file_name": "/users/shouvikm/data/Scale/SCALE_leukemia_01202023/fastqs_after_scATAC_Scale_pipeline/S701-S706/S705/S705P_S5_L003_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7730PTDV/",
"accession": "IGVFFI7730PTDV",
"aliases": [
"maya-kasowski:Scale_scATAC_lane2_R1"
],
"content_type": "reads",
"controlled_access": true,
"creation_timestamp": "2025-03-07T21:42:45.062652+00:00",
"file_format": "fastq",
"file_size": 32103368629,
"href": "/sequence-files/IGVFFI7730PTDV/@@download/IGVFFI7730PTDV.fastq.gz",
"s3_uri": "s3://igvf-restricted-files/2025/03/07/9b4083e0-7541-49fe-9622-aaa774c744e2/IGVFFI7730PTDV.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008637/",
"status": "released",
"term_name": "Illumina NovaSeq 6000"
},
"status": "preview",
"submitted_file_name": "/users/shouvikm/data/Scale/SCALE_leukemia_01202023/fastqs_after_scATAC_Scale_pipeline/S701-S706/S702/S702P_S2_L003_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9350NWNT/",
"accession": "IGVFFI9350NWNT",
"aliases": [
"maya-kasowski:Scale_scATAC_lane2_R2"
],
"content_type": "reads",
"controlled_access": true,
"creation_timestamp": "2025-03-07T21:51:40.267483+00:00",
"file_format": "fastq",
"file_size": 40669614550,
"href": "/sequence-files/IGVFFI9350NWNT/@@download/IGVFFI9350NWNT.fastq.gz",
"s3_uri": "s3://igvf-restricted-files/2025/03/07/b9700253-bac8-494f-adec-8232aaa1fd15/IGVFFI9350NWNT.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008637/",
"status": "released",
"term_name": "Illumina NovaSeq 6000"
},
"status": "preview",
"submitted_file_name": "/users/shouvikm/data/Scale/SCALE_leukemia_01202023/fastqs_after_scATAC_Scale_pipeline/S701-S706/S702/S702P_S2_L003_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3361KDGU/",
"accession": "IGVFFI3361KDGU",
"aliases": [
"maya-kasowski:Scale_scATAC_lane3_I2"
],
"content_type": "reads",
"controlled_access": true,
"creation_timestamp": "2025-03-07T22:04:24.116950+00:00",
"file_format": "fastq",
"file_size": 13230460481,
"href": "/sequence-files/IGVFFI3361KDGU/@@download/IGVFFI3361KDGU.fastq.gz",
"s3_uri": "s3://igvf-restricted-files/2025/03/07/c98ef166-95f8-4e72-9a1d-53cf1861a90c/IGVFFI3361KDGU.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008637/",
"status": "released",
"term_name": "Illumina NovaSeq 6000"
},
"status": "preview",
"submitted_file_name": "/users/shouvikm/data/Scale/SCALE_leukemia_01202023/fastqs_after_scATAC_Scale_pipeline/S701-S706/S703/S703P_S3_L003_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4003TGJY/",
"accession": "IGVFFI4003TGJY",
"aliases": [
"maya-kasowski:Scale_scATAC_lane3_R2"
],
"content_type": "reads",
"controlled_access": true,
"creation_timestamp": "2025-03-07T22:15:17.469360+00:00",
"file_format": "fastq",
"file_size": 43177778727,
"href": "/sequence-files/IGVFFI4003TGJY/@@download/IGVFFI4003TGJY.fastq.gz",
"s3_uri": "s3://igvf-restricted-files/2025/03/07/057e646d-b7e8-49d2-b3ef-ac03e24b1c5b/IGVFFI4003TGJY.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008637/",
"status": "released",
"term_name": "Illumina NovaSeq 6000"
},
"status": "preview",
"submitted_file_name": "/users/shouvikm/data/Scale/SCALE_leukemia_01202023/fastqs_after_scATAC_Scale_pipeline/S701-S706/S703/S703P_S3_L003_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1148TXMZ/",
"accession": "IGVFFI1148TXMZ",
"aliases": [
"maya-kasowski:Scale_scATAC_lane6_I1"
],
"content_type": "reads",
"controlled_access": true,
"creation_timestamp": "2025-03-07T23:12:24.542766+00:00",
"file_format": "fastq",
"file_size": 9672261889,
"href": "/sequence-files/IGVFFI1148TXMZ/@@download/IGVFFI1148TXMZ.fastq.gz",
"s3_uri": "s3://igvf-restricted-files/2025/03/07/b114de64-d2f2-41ff-b8d0-f19ff8caa523/IGVFFI1148TXMZ.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008637/",
"status": "released",
"term_name": "Illumina NovaSeq 6000"
},
"status": "preview",
"submitted_file_name": "/users/shouvikm/data/Scale/SCALE_leukemia_01202023/fastqs_after_scATAC_Scale_pipeline/S701-S706/S706/S706P_S6_L003_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4919YHUQ/",
"accession": "IGVFFI4919YHUQ",
"aliases": [
"maya-kasowski:Scale_scATAC_lane4_I2"
],
"content_type": "reads",
"controlled_access": true,
"creation_timestamp": "2025-03-07T22:27:17.644400+00:00",
"file_format": "fastq",
"file_size": 12148445752,
"href": "/sequence-files/IGVFFI4919YHUQ/@@download/IGVFFI4919YHUQ.fastq.gz",
"s3_uri": "s3://igvf-restricted-files/2025/03/07/9af62fbf-5245-4329-b947-56979bbc5166/IGVFFI4919YHUQ.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008637/",
"status": "released",
"term_name": "Illumina NovaSeq 6000"
},
"status": "preview",
"submitted_file_name": "/users/shouvikm/data/Scale/SCALE_leukemia_01202023/fastqs_after_scATAC_Scale_pipeline/S701-S706/S704/S704P_S4_L003_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4893CRTK/",
"accession": "IGVFFI4893CRTK",
"aliases": [
"maya-kasowski:Scale_scATAC_lane4_R2"
],
"content_type": "reads",
"controlled_access": true,
"creation_timestamp": "2025-03-07T22:37:34.234109+00:00",
"file_format": "fastq",
"file_size": 40308448478,
"href": "/sequence-files/IGVFFI4893CRTK/@@download/IGVFFI4893CRTK.fastq.gz",
"s3_uri": "s3://igvf-restricted-files/2025/03/07/bc0b8652-290c-47e0-8b6b-c617eaa391e3/IGVFFI4893CRTK.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008637/",
"status": "released",
"term_name": "Illumina NovaSeq 6000"
},
"status": "preview",
"submitted_file_name": "/users/shouvikm/data/Scale/SCALE_leukemia_01202023/fastqs_after_scATAC_Scale_pipeline/S701-S706/S704/S704P_S4_L003_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6964PMSI/",
"accession": "IGVFFI6964PMSI",
"aliases": [
"maya-kasowski:Scale_scATAC_lane5_R1"
],
"content_type": "reads",
"controlled_access": true,
"creation_timestamp": "2025-03-07T22:53:14.995984+00:00",
"file_format": "fastq",
"file_size": 36215985660,
"href": "/sequence-files/IGVFFI6964PMSI/@@download/IGVFFI6964PMSI.fastq.gz",
"s3_uri": "s3://igvf-restricted-files/2025/03/07/e4c23f54-31a4-460a-aba2-e3ecf53ce548/IGVFFI6964PMSI.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008637/",
"status": "released",
"term_name": "Illumina NovaSeq 6000"
},
"status": "preview",
"submitted_file_name": "/users/shouvikm/data/Scale/SCALE_leukemia_01202023/fastqs_after_scATAC_Scale_pipeline/S701-S706/S705/S705P_S5_L003_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6310TFWS/",
"accession": "IGVFFI6310TFWS",
"aliases": [
"maya-kasowski:Scale_scATAC_lane6_I2"
],
"content_type": "reads",
"controlled_access": true,
"creation_timestamp": "2025-03-07T23:14:43.608481+00:00",
"file_format": "fastq",
"file_size": 13259686111,
"href": "/sequence-files/IGVFFI6310TFWS/@@download/IGVFFI6310TFWS.fastq.gz",
"s3_uri": "s3://igvf-restricted-files/2025/03/07/6b48dd58-baea-4a3d-b1fb-2e079e332a49/IGVFFI6310TFWS.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008637/",
"status": "released",
"term_name": "Illumina NovaSeq 6000"
},
"status": "preview",
"submitted_file_name": "/users/shouvikm/data/Scale/SCALE_leukemia_01202023/fastqs_after_scATAC_Scale_pipeline/S701-S706/S706/S706P_S6_L003_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7069AMLZ/",
"accession": "IGVFFI7069AMLZ",
"aliases": [
"maya-kasowski:Scale_scATAC_lane6_R1"
],
"content_type": "reads",
"controlled_access": true,
"creation_timestamp": "2025-03-07T23:17:55.433836+00:00",
"file_format": "fastq",
"file_size": 34280660627,
"href": "/sequence-files/IGVFFI7069AMLZ/@@download/IGVFFI7069AMLZ.fastq.gz",
"s3_uri": "s3://igvf-restricted-files/2025/03/07/e50fbaf8-ec13-4da2-9923-2cb33f4b1783/IGVFFI7069AMLZ.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008637/",
"status": "released",
"term_name": "Illumina NovaSeq 6000"
},
"status": "preview",
"submitted_file_name": "/users/shouvikm/data/Scale/SCALE_leukemia_01202023/fastqs_after_scATAC_Scale_pipeline/S701-S706/S706/S706P_S6_L003_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5012UHJY/",
"accession": "IGVFFI5012UHJY",
"aliases": [
"maya-kasowski:Scale_scATAC_lane6_R2"
],
"content_type": "reads",
"controlled_access": true,
"creation_timestamp": "2025-03-07T23:25:40.045955+00:00",
"file_format": "fastq",
"file_size": 43724249635,
"href": "/sequence-files/IGVFFI5012UHJY/@@download/IGVFFI5012UHJY.fastq.gz",
"s3_uri": "s3://igvf-restricted-files/2025/03/07/4ca16433-c45d-4b51-a284-ca569771f26e/IGVFFI5012UHJY.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008637/",
"status": "released",
"term_name": "Illumina NovaSeq 6000"
},
"status": "preview",
"submitted_file_name": "/users/shouvikm/data/Scale/SCALE_leukemia_01202023/fastqs_after_scATAC_Scale_pipeline/S701-S706/S706/S706P_S6_L003_R2_001.fastq.gz",
"upload_status": "validated"
}
],
"input_for": [],
"lab": {
"@id": "/labs/maya-kasowski/",
"title": "Maya Kasowski, Stanford"
},
"preferred_assay_title": "scATAC-seq",
"protocols": [
"https://www.protocols.io/view/scatac-pre-indexing-kit-10x-scatac-seq-n92ld5bj8v5b/v1"
],
"samples": [
{
"@id": "/multiplexed-samples/IGVFSM1625LLXE/",
"@type": [
"MultiplexedSample",
"Sample",
"Item"
],
"accession": "IGVFSM1625LLXE",
"aliases": [
"maya-kasowski:multiplexed_samples_Scale",
"maya-kasowski:multiplexed_samples_Scale_scATAC"
],
"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": "2025-03-07T20:36:18.987147+00:00",
"summary": "scATAC-seq",
"uuid": "b44d0fde-bc48-4bab-a64f-3e5082b20a77"
}