{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS6310VXMX/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS6310VXMX",
"aliases": [
"ansuman-satpathy:snATAC-seq_igvf6_10x2"
],
"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/IGVFDS7320EONJ/",
"accession": "IGVFDS7320EONJ",
"aliases": [
"ansuman-satpathy:multiseq_igvf6_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": [],
"creation_timestamp": "2024-07-22T00:31:54.601265+00:00",
"donors": [
{
"@id": "/human-donors/IGVFDO6638HIAD/",
"accession": "IGVFDO6638HIAD",
"aliases": [
"igvf:donor_of_H1"
],
"sex": "male",
"status": "released",
"taxa": "Homo sapiens"
}
],
"externally_hosted": false,
"file_set_type": "experimental data",
"files": [
{
"@id": "/sequence-files/IGVFFI4744MLNT/",
"accession": "IGVFFI4744MLNT",
"aliases": [
"ansuman-satpathy:igvf_exp6_atac_10x2_NGS1_i1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-07-22T17:31:00.188050+00:00",
"file_format": "fastq",
"file_size": 1907415241,
"href": "/sequence-files/IGVFFI4744MLNT/@@download/IGVFFI4744MLNT.fastq.gz",
"s3_uri": "s3://igvf-files/2024/07/22/d51d22d3-7dcd-4056-9bbd-cb68b0d75614/IGVFFI4744MLNT.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_IGVF6_McGinnis/ATAC/FASTQ/ATAC_2_S6_L005_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0421GTEH/",
"accession": "IGVFFI0421GTEH",
"aliases": [
"ansuman-satpathy:igvf_exp6_atac_10x2_NGS2_i1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-07-22T20:53:25.786813+00:00",
"file_format": "fastq",
"file_size": 1915653142,
"href": "/sequence-files/IGVFFI0421GTEH/@@download/IGVFFI0421GTEH.fastq.gz",
"s3_uri": "s3://igvf-files/2024/07/22/0bb5705e-be38-4b0c-abb6-818d6bc7dfe7/IGVFFI0421GTEH.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_IGVF6_McGinnis/ATAC/FASTQ/ATAC_2_S6_L006_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4067LHOZ/",
"accession": "IGVFFI4067LHOZ",
"aliases": [
"ansuman-satpathy:igvf_exp6_atac_10x2_NGS1_r2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-07-22T17:29:41.744274+00:00",
"file_format": "fastq",
"file_size": 4379133868,
"href": "/sequence-files/IGVFFI4067LHOZ/@@download/IGVFFI4067LHOZ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/07/22/5bc85ff2-70dd-40d9-9d3a-deea62ff95e8/IGVFFI4067LHOZ.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_IGVF6_McGinnis/ATAC/FASTQ/ATAC_2_S6_L005_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6420ORAF/",
"accession": "IGVFFI6420ORAF",
"aliases": [
"ansuman-satpathy:igvf_exp6_atac_10x2_NGS3_i1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-07-22T20:56:14.756519+00:00",
"file_format": "fastq",
"file_size": 1935360745,
"href": "/sequence-files/IGVFFI6420ORAF/@@download/IGVFFI6420ORAF.fastq.gz",
"s3_uri": "s3://igvf-files/2024/07/22/1eb08ec6-59f9-4c25-8820-1ca29f9f4cda/IGVFFI6420ORAF.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_IGVF6_McGinnis/ATAC/FASTQ/ATAC_2_S6_L007_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1239EPAD/",
"accession": "IGVFFI1239EPAD",
"aliases": [
"ansuman-satpathy:igvf_exp6_atac_10x2_NGS2_r2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-07-22T20:48:25.552548+00:00",
"file_format": "fastq",
"file_size": 4402848243,
"href": "/sequence-files/IGVFFI1239EPAD/@@download/IGVFFI1239EPAD.fastq.gz",
"s3_uri": "s3://igvf-files/2024/07/22/69a3f861-2e3c-485b-a6e4-f10612b89984/IGVFFI1239EPAD.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_IGVF6_McGinnis/ATAC/FASTQ/ATAC_2_S6_L006_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0428TBOI/",
"accession": "IGVFFI0428TBOI",
"aliases": [
"ansuman-satpathy:igvf_exp6_atac_10x2_NGS3_r3"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-07-22T20:55:31.126424+00:00",
"file_format": "fastq",
"file_size": 8238758696,
"href": "/sequence-files/IGVFFI0428TBOI/@@download/IGVFFI0428TBOI.fastq.gz",
"s3_uri": "s3://igvf-files/2024/07/22/38083239-037f-4d40-a895-d00b68a2d53d/IGVFFI0428TBOI.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_IGVF6_McGinnis/ATAC/FASTQ/ATAC_2_S6_L007_R3_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8454EYKE/",
"accession": "IGVFFI8454EYKE",
"aliases": [
"ansuman-satpathy:igvf_exp6_atac_10x2_NGS1_r3"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-07-22T17:30:20.365177+00:00",
"file_format": "fastq",
"file_size": 8072032432,
"href": "/sequence-files/IGVFFI8454EYKE/@@download/IGVFFI8454EYKE.fastq.gz",
"s3_uri": "s3://igvf-files/2024/07/22/fe98365d-1f75-484e-8570-dc82e425500a/IGVFFI8454EYKE.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_IGVF6_McGinnis/ATAC/FASTQ/ATAC_2_S6_L005_R3_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9585RVDY/",
"accession": "IGVFFI9585RVDY",
"aliases": [
"ansuman-satpathy:igvf_exp6_atac_10x2_NGS2_r3"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-07-22T20:49:06.622533+00:00",
"file_format": "fastq",
"file_size": 8098725039,
"href": "/sequence-files/IGVFFI9585RVDY/@@download/IGVFFI9585RVDY.fastq.gz",
"s3_uri": "s3://igvf-files/2024/07/22/699a1df3-3232-4e8f-a1fb-3f18ffe7ddf5/IGVFFI9585RVDY.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_IGVF6_McGinnis/ATAC/FASTQ/ATAC_2_S6_L006_R3_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2077YAUW/",
"accession": "IGVFFI2077YAUW",
"aliases": [
"ansuman-satpathy:igvf_exp6_atac_10x2_NGS3_r1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-07-22T20:53:55.653621+00:00",
"file_format": "fastq",
"file_size": 8300752604,
"href": "/sequence-files/IGVFFI2077YAUW/@@download/IGVFFI2077YAUW.fastq.gz",
"s3_uri": "s3://igvf-files/2024/07/22/6a4c91cc-73a2-4a29-9ab3-08475540d48c/IGVFFI2077YAUW.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_IGVF6_McGinnis/ATAC/FASTQ/ATAC_2_S6_L007_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2655RSJT/",
"accession": "IGVFFI2655RSJT",
"aliases": [
"ansuman-satpathy:igvf_exp6_atac_10x2_NGS3_r2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-07-22T20:54:39.465602+00:00",
"file_format": "fastq",
"file_size": 4478262979,
"href": "/sequence-files/IGVFFI2655RSJT/@@download/IGVFFI2655RSJT.fastq.gz",
"s3_uri": "s3://igvf-files/2024/07/22/ac53e13a-0796-4047-bf2b-3799c1630f25/IGVFFI2655RSJT.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_IGVF6_McGinnis/ATAC/FASTQ/ATAC_2_S6_L007_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1104DNVL/",
"accession": "IGVFFI1104DNVL",
"aliases": [
"ansuman-satpathy:igvf_exp6_atac_10x2_NGS1_r1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-07-22T17:28:41.429658+00:00",
"file_format": "fastq",
"file_size": 8143525387,
"href": "/sequence-files/IGVFFI1104DNVL/@@download/IGVFFI1104DNVL.fastq.gz",
"s3_uri": "s3://igvf-files/2024/07/22/8751ab37-2ccb-4369-ba5a-5b9bb05af0c0/IGVFFI1104DNVL.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_IGVF6_McGinnis/ATAC/FASTQ/ATAC_2_S6_L005_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4654CECJ/",
"accession": "IGVFFI4654CECJ",
"aliases": [
"ansuman-satpathy:igvf_exp6_atac_10x2_NGS2_r1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-07-22T17:31:28.502675+00:00",
"file_format": "fastq",
"file_size": 8187612770,
"href": "/sequence-files/IGVFFI4654CECJ/@@download/IGVFFI4654CECJ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/07/22/358ad8d3-43e0-4843-b648-a53424a8752e/IGVFFI4654CECJ.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_IGVF6_McGinnis/ATAC/FASTQ/ATAC_2_S6_L006_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI1904XWMX/",
"accession": "IGVFFI1904XWMX",
"aliases": [
"ansuman-satpathy:seqspec_igvf_exp6_atac_10x2_NGS2"
],
"content_type": "seqspec",
"creation_timestamp": "2024-09-18T02:41:46.417584+00:00",
"file_format": "yaml",
"file_size": 1377,
"href": "/configuration-files/IGVFFI1904XWMX/@@download/IGVFFI1904XWMX.yaml.gz",
"s3_uri": "s3://igvf-files/2024/09/18/123b6476-83e2-4f20-a15f-dbabfe5ac449/IGVFFI1904XWMX.yaml.gz",
"status": "released",
"submitted_file_name": "/home/users/cmcginni/igvf_utils_out/seqspec/igvf_exp6_atac_10x2_NGS2_atac_seqspec.yaml.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI6265KQCD/",
"accession": "IGVFFI6265KQCD",
"aliases": [
"ansuman-satpathy:seqspec_igvf_exp6_atac_10x2_NGS1"
],
"content_type": "seqspec",
"creation_timestamp": "2024-09-18T02:41:42.591519+00:00",
"file_format": "yaml",
"file_size": 1380,
"href": "/configuration-files/IGVFFI6265KQCD/@@download/IGVFFI6265KQCD.yaml.gz",
"s3_uri": "s3://igvf-files/2024/09/18/15bb8fc5-2652-4e16-b7f4-1b2df5251898/IGVFFI6265KQCD.yaml.gz",
"status": "released",
"submitted_file_name": "/home/users/cmcginni/igvf_utils_out/seqspec/igvf_exp6_atac_10x2_NGS1_atac_seqspec.yaml.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI0603MXUI/",
"accession": "IGVFFI0603MXUI",
"aliases": [
"ansuman-satpathy:seqspec_igvf_exp6_atac_10x2_NGS3"
],
"content_type": "seqspec",
"creation_timestamp": "2024-09-18T02:41:50.346503+00:00",
"file_format": "yaml",
"file_size": 1376,
"href": "/configuration-files/IGVFFI0603MXUI/@@download/IGVFFI0603MXUI.yaml.gz",
"s3_uri": "s3://igvf-files/2024/09/18/b79bbaf2-4507-4903-a965-5357549c3ab6/IGVFFI0603MXUI.yaml.gz",
"status": "released",
"submitted_file_name": "/home/users/cmcginni/igvf_utils_out/seqspec/igvf_exp6_atac_10x2_NGS3_atac_seqspec.yaml.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS3232NVVG/"
],
"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/IGVFDS4095FWRD/",
"accession": "IGVFDS4095FWRD",
"status": "released"
}
],
"release_timestamp": "2025-03-07T01:12:43.179979+00:00",
"samples": [
{
"@id": "/multiplexed-samples/IGVFSM8961ZZQN/",
"@type": [
"MultiplexedSample",
"Sample",
"Item"
],
"accession": "IGVFSM8961ZZQN",
"aliases": [
"ansuman-satpathy:multiplexed_sample_igvf6_10x2"
],
"classifications": [
"cell line",
"differentiated cell specimen",
"multiplexed sample"
],
"disease_terms": [],
"institutional_certificates": [],
"modifications": [],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0003042/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"aliases": [
"igvf:H1"
],
"status": "released",
"summary": "H1-hESC",
"term_name": "H1-hESC"
}
],
"status": "released",
"summary": "multiplexed sample: H1-hESC differentiated cell specimen induced to islet of Langerhans for 18 days, male, Homo sapiens; H1-hESC differentiated cell specimen induced to islet of Langerhans for 7 days, male, Homo sapiens; ... and 6 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": "2024-07-22T17:01:32.849746+00:00",
"summary": "single-nucleus ATAC-seq (10x multiome with MULTI-seq)",
"uuid": "91d81e3e-3ffe-4266-9e97-c661a115e8bd"
}