{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS5893VQJY/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS5893VQJY",
"aliases": [
"ansuman-satpathy:snATAC-seq_igvf3_10x1"
],
"assay_term": {
"@id": "/assay-terms/OBI_0002762/",
"assay_slims": [
"chromatin accessibility"
],
"status": "released",
"term_name": "single-nucleus ATAC-seq"
},
"audit": {},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS8334UDJX/",
"accession": "IGVFDS8334UDJX",
"aliases": [
"ansuman-satpathy:multiseq_igvf3_10x1"
],
"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": [],
"creation_timestamp": "2024-07-21T23:09:36.125783+00:00",
"donors": [
{
"@id": "/human-donors/IGVFDO2718IDDQ/",
"accession": "IGVFDO2718IDDQ",
"aliases": [
"igvf:donor_of_H9"
],
"sex": "female",
"status": "released",
"taxa": "Homo sapiens"
},
{
"@id": "/human-donors/IGVFDO1756PPKO/",
"accession": "IGVFDO1756PPKO",
"aliases": [
"igvf:donor_of_WTC11"
],
"sex": "male",
"status": "released",
"taxa": "Homo sapiens"
},
{
"@id": "/human-donors/IGVFDO2837BRET/",
"accession": "IGVFDO2837BRET",
"aliases": [
"igvf:donor_of_HepG2"
],
"sex": "male",
"status": "released",
"taxa": "Homo sapiens"
}
],
"externally_hosted": false,
"file_set_type": "experimental data",
"files": [
{
"@id": "/sequence-files/IGVFFI9903KSHL/",
"accession": "IGVFFI9903KSHL",
"aliases": [
"ansuman-satpathy:igvf_exp3_atac_10x1_NGS1_i1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-07-21T23:36:23.052799+00:00",
"file_format": "fastq",
"file_size": 2142448687,
"href": "/sequence-files/IGVFFI9903KSHL/@@download/IGVFFI9903KSHL.fastq.gz",
"s3_uri": "s3://igvf-files/2024/07/21/b5b85542-91d8-4c81-9cb4-2b3db9ebd731/IGVFFI9903KSHL.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_IGVF3_McGinnis/ATAC/FASTQ/ATAC_1-_S1_L001_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5622EDZO/",
"accession": "IGVFFI5622EDZO",
"aliases": [
"ansuman-satpathy:igvf_exp3_atac_10x1_NGS2_r1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-07-21T23:36:56.596346+00:00",
"file_format": "fastq",
"file_size": 9011025731,
"href": "/sequence-files/IGVFFI5622EDZO/@@download/IGVFFI5622EDZO.fastq.gz",
"s3_uri": "s3://igvf-files/2024/07/21/3cfbb0a7-d034-4c4e-bd4a-fda0d215927c/IGVFFI5622EDZO.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_IGVF3_McGinnis/ATAC/FASTQ/ATAC_1-_S1_L002_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5188FQQU/",
"accession": "IGVFFI5188FQQU",
"aliases": [
"ansuman-satpathy:igvf_exp3_atac_10x1_NGS2_i1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-07-21T23:40:00.990668+00:00",
"file_format": "fastq",
"file_size": 2186600769,
"href": "/sequence-files/IGVFFI5188FQQU/@@download/IGVFFI5188FQQU.fastq.gz",
"s3_uri": "s3://igvf-files/2024/07/21/1f86489b-cb78-4e5a-8dd6-3f85214ed676/IGVFFI5188FQQU.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_IGVF3_McGinnis/ATAC/FASTQ/ATAC_1-_S1_L002_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0059KQUU/",
"accession": "IGVFFI0059KQUU",
"aliases": [
"ansuman-satpathy:igvf_exp3_atac_10x1_NGS1_r2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-07-21T23:34:31.857671+00:00",
"file_format": "fastq",
"file_size": 4761644732,
"href": "/sequence-files/IGVFFI0059KQUU/@@download/IGVFFI0059KQUU.fastq.gz",
"s3_uri": "s3://igvf-files/2024/07/21/a7bae7f9-077d-4fcc-80be-96b961b3fcee/IGVFFI0059KQUU.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_IGVF3_McGinnis/ATAC/FASTQ/ATAC_1-_S1_L001_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3240KMDW/",
"accession": "IGVFFI3240KMDW",
"aliases": [
"ansuman-satpathy:igvf_exp3_atac_10x1_NGS1_r3"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-07-21T23:35:23.921146+00:00",
"file_format": "fastq",
"file_size": 8898401574,
"href": "/sequence-files/IGVFFI3240KMDW/@@download/IGVFFI3240KMDW.fastq.gz",
"s3_uri": "s3://igvf-files/2024/07/21/2697c999-9b3a-43bf-bea2-d889e332860e/IGVFFI3240KMDW.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_IGVF3_McGinnis/ATAC/FASTQ/ATAC_1-_S1_L001_R3_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8805ZTIW/",
"accession": "IGVFFI8805ZTIW",
"aliases": [
"ansuman-satpathy:igvf_exp3_atac_10x1_NGS1_r1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-07-21T23:33:20.131088+00:00",
"file_format": "fastq",
"file_size": 8893949466,
"href": "/sequence-files/IGVFFI8805ZTIW/@@download/IGVFFI8805ZTIW.fastq.gz",
"s3_uri": "s3://igvf-files/2024/07/21/3f7b36e5-2e08-405f-82f4-558e303b4c62/IGVFFI8805ZTIW.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_IGVF3_McGinnis/ATAC/FASTQ/ATAC_1-_S1_L001_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1873DKIW/",
"accession": "IGVFFI1873DKIW",
"aliases": [
"ansuman-satpathy:igvf_exp3_atac_10x1_NGS2_r2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-07-21T23:38:00.277828+00:00",
"file_format": "fastq",
"file_size": 4836213445,
"href": "/sequence-files/IGVFFI1873DKIW/@@download/IGVFFI1873DKIW.fastq.gz",
"s3_uri": "s3://igvf-files/2024/07/21/9de94f0f-b2ff-4fd6-83c9-38273c5d0245/IGVFFI1873DKIW.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_IGVF3_McGinnis/ATAC/FASTQ/ATAC_1-_S1_L002_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2745JXTS/",
"accession": "IGVFFI2745JXTS",
"aliases": [
"ansuman-satpathy:igvf_exp3_atac_10x1_NGS2_r3"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-07-21T23:39:01.858604+00:00",
"file_format": "fastq",
"file_size": 9034680465,
"href": "/sequence-files/IGVFFI2745JXTS/@@download/IGVFFI2745JXTS.fastq.gz",
"s3_uri": "s3://igvf-files/2024/07/21/090b8e47-ade9-48ac-a192-b46955e6be33/IGVFFI2745JXTS.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_IGVF3_McGinnis/ATAC/FASTQ/ATAC_1-_S1_L002_R3_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI4852WGBH/",
"accession": "IGVFFI4852WGBH",
"aliases": [
"ansuman-satpathy:seqspec_igvf_exp3_atac_10x1_NGS1"
],
"content_type": "seqspec",
"creation_timestamp": "2024-09-18T02:35:59.409086+00:00",
"file_format": "yaml",
"file_size": 1376,
"href": "/configuration-files/IGVFFI4852WGBH/@@download/IGVFFI4852WGBH.yaml.gz",
"s3_uri": "s3://igvf-files/2024/09/18/e3e15466-2270-4eed-858b-1b7d9323310b/IGVFFI4852WGBH.yaml.gz",
"status": "released",
"submitted_file_name": "/home/users/cmcginni/igvf_utils_out/seqspec/igvf_exp3_atac_10x1_NGS1_atac_seqspec.yaml.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI7989MQJF/",
"accession": "IGVFFI7989MQJF",
"aliases": [
"ansuman-satpathy:seqspec_igvf_exp3_atac_10x1_NGS2"
],
"content_type": "seqspec",
"creation_timestamp": "2024-09-18T02:36:03.382533+00:00",
"file_format": "yaml",
"file_size": 1372,
"href": "/configuration-files/IGVFFI7989MQJF/@@download/IGVFFI7989MQJF.yaml.gz",
"s3_uri": "s3://igvf-files/2024/09/18/abe4b006-9c5d-48cb-847d-2704938cf525/IGVFFI7989MQJF.yaml.gz",
"status": "released",
"submitted_file_name": "/home/users/cmcginni/igvf_utils_out/seqspec/igvf_exp3_atac_10x1_NGS2_atac_seqspec.yaml.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS9170BNTS/"
],
"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/IGVFDS2000OICT/",
"accession": "IGVFDS2000OICT",
"status": "released"
}
],
"release_timestamp": "2025-03-07T01:10:49.004082+00:00",
"samples": [
{
"@id": "/multiplexed-samples/IGVFSM4259POAT/",
"@type": [
"MultiplexedSample",
"Sample",
"Item"
],
"accession": "IGVFSM4259POAT",
"aliases": [
"ansuman-satpathy:multiplexed_sample_igvf3_10x1"
],
"classifications": [
"cell line",
"differentiated cell specimen",
"multiplexed sample"
],
"disease_terms": [],
"institutional_certificates": [],
"modifications": [],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0001187/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"aliases": [
"igvf:HepG2"
],
"status": "released",
"summary": "HepG2",
"term_name": "HepG2"
},
{
"@id": "/sample-terms/EFO_0003045/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"aliases": [
"igvf:H9"
],
"status": "released",
"summary": "H9",
"term_name": "H9"
},
{
"@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: H9 differentiated cell specimen induced to cardiac muscle cell for 15 days, female, Homo sapiens; HepG2 cell line, male, Homo sapiens grown in DMEM without serum; ... and 10 more samples",
"taxa": "Homo sapiens",
"treatments": []
}
],
"schema_version": "25",
"status": "released",
"submitted_by": {
"@id": "/users/353655bc-31a1-4cd9-bac3-c7d34faf722f/",
"title": "Christopher Mcginnis"
},
"submitted_files_timestamp": "2024-07-21T23:27:16.837181+00:00",
"summary": "single-nucleus ATAC-seq (10x multiome with MULTI-seq)",
"uuid": "db4eb24c-6b18-4f54-bd2c-0e64fecb5a2a"
}