{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS6995DUBD/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS6995DUBD",
"aliases": [
"ansuman-satpathy:snATAC-seq_igvf4_10x2"
],
"assay_term": {
"@id": "/assay-terms/OBI_0002762/",
"assay_slims": [
"chromatin accessibility"
],
"status": "released",
"term_name": "single-nucleus ATAC-seq"
},
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing publication",
"detail": "Auxiliary set [IGVFDS6940QNAZ](/auxiliary-sets/IGVFDS6940QNAZ/) 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": "/auxiliary-sets/IGVFDS6940QNAZ/"
},
{
"category": "missing publication",
"detail": "Multiplexed sample [IGVFSM7068ZFMY](/multiplexed-samples/IGVFSM7068ZFMY/) 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": "/multiplexed-samples/IGVFSM7068ZFMY/"
},
{
"category": "missing publication",
"detail": "Measurement set [IGVFDS6995DUBD](/measurement-sets/IGVFDS6995DUBD/) 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/IGVFDS6995DUBD/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing strand specificity",
"detail": "Measurement set [IGVFDS6995DUBD](/measurement-sets/IGVFDS6995DUBD/) 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/IGVFDS6995DUBD/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS6940QNAZ/",
"accession": "IGVFDS6940QNAZ",
"aliases": [
"ansuman-satpathy:multiseq_igvf4_10x2"
],
"file_set_type": "lipid-conjugated oligo sequencing",
"status": "released"
}
],
"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": false,
"creation_timestamp": "2024-07-21T23:21:37.722759+00:00",
"data_use_limitation_summaries": [
"No limitations"
],
"donors": [
{
"@id": "/human-donors/IGVFDO1756PPKO/",
"accession": "IGVFDO1756PPKO",
"aliases": [
"igvf:donor_of_WTC11"
],
"sex": "male",
"status": "released",
"taxa": "Homo sapiens"
}
],
"externally_hosted": false,
"file_set_type": "experimental data",
"files": [
{
"@id": "/sequence-files/IGVFFI7313NUEB/",
"accession": "IGVFFI7313NUEB",
"aliases": [
"ansuman-satpathy:igvf_exp4_atac_10x2_NGS1_i1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-07-22T00:24:34.926460+00:00",
"file_format": "fastq",
"file_size": 4129270075,
"href": "/sequence-files/IGVFFI7313NUEB/@@download/IGVFFI7313NUEB.fastq.gz",
"s3_uri": "s3://igvf-files/2024/07/22/aa1fc438-48c6-4fa6-b44b-da8105fa1197/IGVFFI7313NUEB.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "released",
"submitted_file_name": "/oak/stanford/projects/igvf/Projects/230522_IGVF4_McGinnis/ATAC/FASTQ/_ATAC_2_S6_L003_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2036ECMB/",
"accession": "IGVFFI2036ECMB",
"aliases": [
"ansuman-satpathy:igvf_exp4_atac_10x2_NGS1_r1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-07-22T00:25:31.286763+00:00",
"file_format": "fastq",
"file_size": 19587410813,
"href": "/sequence-files/IGVFFI2036ECMB/@@download/IGVFFI2036ECMB.fastq.gz",
"s3_uri": "s3://igvf-files/2024/07/22/bb779554-66c7-453c-8cf3-a500fafc6878/IGVFFI2036ECMB.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "released",
"submitted_file_name": "/oak/stanford/projects/igvf/Projects/230522_IGVF4_McGinnis/ATAC/FASTQ/_ATAC_2_S6_L003_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6631RXKI/",
"accession": "IGVFFI6631RXKI",
"aliases": [
"ansuman-satpathy:igvf_exp4_atac_10x2_NGS1_r2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-07-22T00:26:59.552306+00:00",
"file_format": "fastq",
"file_size": 10731256466,
"href": "/sequence-files/IGVFFI6631RXKI/@@download/IGVFFI6631RXKI.fastq.gz",
"s3_uri": "s3://igvf-files/2024/07/22/42f9027e-ab80-4447-a141-29ca5636e00f/IGVFFI6631RXKI.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "released",
"submitted_file_name": "/oak/stanford/projects/igvf/Projects/230522_IGVF4_McGinnis/ATAC/FASTQ/_ATAC_2_S6_L003_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3571ZWPJ/",
"accession": "IGVFFI3571ZWPJ",
"aliases": [
"ansuman-satpathy:igvf_exp4_atac_10x2_NGS2_i1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-07-22T00:29:30.768959+00:00",
"file_format": "fastq",
"file_size": 4094963424,
"href": "/sequence-files/IGVFFI3571ZWPJ/@@download/IGVFFI3571ZWPJ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/07/22/f339da85-c65a-466f-8fe1-6c75cb7cd593/IGVFFI3571ZWPJ.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "released",
"submitted_file_name": "/oak/stanford/projects/igvf/Projects/230522_IGVF4_McGinnis/ATAC/FASTQ/_ATAC_2_S6_L004_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8805HERJ/",
"accession": "IGVFFI8805HERJ",
"aliases": [
"ansuman-satpathy:igvf_exp4_atac_10x2_NGS2_r1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-07-22T00:30:25.177855+00:00",
"file_format": "fastq",
"file_size": 19475879335,
"href": "/sequence-files/IGVFFI8805HERJ/@@download/IGVFFI8805HERJ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/07/22/0df96bf4-3a37-4db6-a90e-d5fad4a460a9/IGVFFI8805HERJ.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "released",
"submitted_file_name": "/oak/stanford/projects/igvf/Projects/230522_IGVF4_McGinnis/ATAC/FASTQ/_ATAC_2_S6_L004_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7329CJCL/",
"accession": "IGVFFI7329CJCL",
"aliases": [
"ansuman-satpathy:igvf_exp4_atac_10x2_NGS2_r2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-07-22T00:31:50.331046+00:00",
"file_format": "fastq",
"file_size": 10635644105,
"href": "/sequence-files/IGVFFI7329CJCL/@@download/IGVFFI7329CJCL.fastq.gz",
"s3_uri": "s3://igvf-files/2024/07/22/13a0ebff-8b6b-4841-8804-1ee4f585d320/IGVFFI7329CJCL.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "released",
"submitted_file_name": "/oak/stanford/projects/igvf/Projects/230522_IGVF4_McGinnis/ATAC/FASTQ/_ATAC_2_S6_L004_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0104HBOM/",
"accession": "IGVFFI0104HBOM",
"aliases": [
"ansuman-satpathy:igvf_exp4_atac_10x2_NGS1_r3"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-07-22T00:28:14.824914+00:00",
"file_format": "fastq",
"file_size": 19688535368,
"href": "/sequence-files/IGVFFI0104HBOM/@@download/IGVFFI0104HBOM.fastq.gz",
"s3_uri": "s3://igvf-files/2024/07/22/39002f84-e44e-4b26-b8ae-386b1e46dc4e/IGVFFI0104HBOM.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "released",
"submitted_file_name": "/oak/stanford/projects/igvf/Projects/230522_IGVF4_McGinnis/ATAC/FASTQ/_ATAC_2_S6_L003_R3_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8315YWHU/",
"accession": "IGVFFI8315YWHU",
"aliases": [
"ansuman-satpathy:igvf_exp4_atac_10x2_NGS2_r3"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-07-22T00:33:09.752318+00:00",
"file_format": "fastq",
"file_size": 19510023252,
"href": "/sequence-files/IGVFFI8315YWHU/@@download/IGVFFI8315YWHU.fastq.gz",
"s3_uri": "s3://igvf-files/2024/07/22/2acf6ca8-cea4-4e98-b3e5-bbdcd80f9d0c/IGVFFI8315YWHU.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "released",
"submitted_file_name": "/oak/stanford/projects/igvf/Projects/230522_IGVF4_McGinnis/ATAC/FASTQ/_ATAC_2_S6_L004_R3_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI1276MPAQ/",
"accession": "IGVFFI1276MPAQ",
"aliases": [
"ansuman-satpathy:seqspec_igvf_exp4_atac_10x2_NGS2"
],
"content_type": "seqspec",
"creation_timestamp": "2024-09-18T02:37:41.854692+00:00",
"file_format": "yaml",
"file_size": 1381,
"href": "/configuration-files/IGVFFI1276MPAQ/@@download/IGVFFI1276MPAQ.yaml.gz",
"s3_uri": "s3://igvf-files/2024/09/18/504ecf07-16ce-4f98-b7e6-a7aa9fbb1be7/IGVFFI1276MPAQ.yaml.gz",
"status": "released",
"submitted_file_name": "/home/users/cmcginni/igvf_utils_out/seqspec/igvf_exp4_atac_10x2_NGS2_atac_seqspec.yaml.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI9651XULX/",
"accession": "IGVFFI9651XULX",
"aliases": [
"ansuman-satpathy:seqspec_igvf_exp4_atac_10x2_NGS1"
],
"content_type": "seqspec",
"creation_timestamp": "2024-09-18T02:37:37.940978+00:00",
"file_format": "yaml",
"file_size": 1373,
"href": "/configuration-files/IGVFFI9651XULX/@@download/IGVFFI9651XULX.yaml.gz",
"s3_uri": "s3://igvf-files/2024/09/18/33a0d7b0-1a4b-41a1-af22-d7a353ed1ebd/IGVFFI9651XULX.yaml.gz",
"status": "released",
"submitted_file_name": "/home/users/cmcginni/igvf_utils_out/seqspec/igvf_exp4_atac_10x2_NGS1_atac_seqspec.yaml.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS3751NDQI/"
],
"lab": {
"@id": "/labs/ansuman-satpathy/",
"title": "Ansuman Satpathy, Stanford"
},
"multiome_size": 2,
"onlist_files": [
"/tabular-files/IGVFFI7587TJLC/"
],
"onlist_method": "no combination",
"preferred_assay_title": "10x multiome with MULTI-seq",
"protocols": [
"https://www.protocols.io/view/multi-seq-for-multiome-igvf-round-2-experiment-1-dfqp3mvn"
],
"related_multiome_datasets": [
{
"@id": "/measurement-sets/IGVFDS8256MZOE/",
"accession": "IGVFDS8256MZOE",
"status": "released"
}
],
"release_timestamp": "2025-03-07T01:11:29.964577+00:00",
"samples": [
{
"@id": "/multiplexed-samples/IGVFSM7068ZFMY/",
"@type": [
"MultiplexedSample",
"Sample",
"Item"
],
"accession": "IGVFSM7068ZFMY",
"aliases": [
"ansuman-satpathy:multiplexed_sample_igvf4_10x2"
],
"classifications": [
"cell line",
"multiplexed sample"
],
"disease_terms": [],
"institutional_certificates": [
{
"@id": "/institutional-certificates/e5598331-9e7c-4bd5-8e7b-64d5a4529006/",
"certificate_identifier": "IP115-21",
"controlled_access": false,
"status": "released"
}
],
"modifications": [],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0009747/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"aliases": [
"igvf:WTC11"
],
"status": "released",
"summary": "GM25256 (WTC-11)",
"term_name": "GM25256 (WTC-11)"
}
],
"status": "released",
"summary": "multiplexed sample: Homo sapiens (male) GM25256 (WTC-11) cell line treated with 50 ng/mL interleukin 4 for 1 day; Homo sapiens (male) GM25256 (WTC-11) cell line treated with 100 ng/mL macrophage colony-stimulating factor 1 for 7 days; ... and 13 more samples",
"taxa": "Homo sapiens",
"treatments": [
{
"@id": "/treatments/2987f643-86dc-4113-af7e-d4b5d162b5c8/",
"purpose": "differentiation",
"status": "in progress",
"summary": "Treatment of 0.025 ng/mL acetylated low density lipoprotein for 1 day",
"treatment_type": "chemical"
},
{
"@id": "/treatments/729630f8-aa05-47f5-9cba-ee7a264da593/",
"purpose": "differentiation",
"status": "in progress",
"summary": "Treatment of 50 ng/mL interleukin 4 for 1 day",
"treatment_type": "protein"
},
{
"@id": "/treatments/ae8065d2-85f3-498e-b4f2-01a38756d48e/",
"purpose": "differentiation",
"status": "in progress",
"summary": "Treatment of 20 ng/mL interferon gamma for 1 day",
"treatment_type": "protein"
},
{
"@id": "/treatments/bec71d5e-97ef-489a-acb7-5336691b6c39/",
"purpose": "differentiation",
"status": "in progress",
"summary": "Treatment of 100 ng/mL macrophage colony-stimulating factor 1 for 7 days",
"treatment_type": "protein"
}
]
}
],
"schema_version": "26",
"status": "released",
"submitted_by": {
"@id": "/users/353655bc-31a1-4cd9-bac3-c7d34faf722f/",
"title": "Christopher Mcginnis"
},
"submitted_files_timestamp": "2024-07-22T00:24:34.926460+00:00",
"summary": "single-nucleus ATAC-seq (10x multiome with MULTI-seq)",
"uuid": "020a66e3-c87e-4a69-ad48-5e29dfc7b2e6"
}