{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS9764OTVQ/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS9764OTVQ",
"aliases": [
"harinder-singh:Bcells_don1_pitt_multiome_scATACseq_day56_measurement"
],
"assay_term": {
"@id": "/assay-terms/OBI_0002762/",
"assay_slims": [
"chromatin accessibility"
],
"status": "released",
"term_name": "single-nucleus ATAC-seq"
},
"audit": {},
"award": {
"@id": "/awards/HG012041/",
"component": "networks",
"contact_pi": {
"@id": "/users/5d389fb5-2279-4778-87ca-c20b8536998f/",
"title": "Harinder Singh"
},
"title": "Linking genome variation to transcriptional network dynamics in human B cells"
},
"control_for": [],
"controlled_access": true,
"creation_timestamp": "2024-11-06T17:10:50.134086+00:00",
"data_use_limitation_summaries": [
"HMB"
],
"donors": [
{
"@id": "/human-donors/IGVFDO9916UELD/",
"accession": "IGVFDO9916UELD",
"aliases": [
"harinder-singh:donor_1"
],
"sex": "male",
"status": "preview",
"taxa": "Homo sapiens"
}
],
"externally_hosted": false,
"file_set_type": "experimental data",
"files": [
{
"@id": "/sequence-files/IGVFFI7567EQCB/",
"accession": "IGVFFI7567EQCB",
"aliases": [
"harinder-singh:donor1_Bcell_multiome_ATAC_NGS_day5_6_L002_I1"
],
"content_type": "reads",
"controlled_access": true,
"creation_timestamp": "2025-03-04T22:13:45.949022+00:00",
"file_format": "fastq",
"file_size": 876770160,
"href": "/sequence-files/IGVFFI7567EQCB/@@download/IGVFFI7567EQCB.fastq.gz",
"md5sum": "f0153bddd52ad3214a949f09ecc6585a",
"s3_uri": "s3://igvf-restricted-files/2025/03/04/7b8a6de6-da27-47f9-b826-ca9ea186adfc/IGVFFI7567EQCB.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008637/",
"status": "released",
"term_name": "Illumina NovaSeq 6000"
},
"status": "preview",
"submitted_file_name": "/ix/djishnu/peasena/primary_multiome/donor1_upmc/fastqs/scATAC/NP002_03_120222_Singh_Multiome_scATAC_remade_SIN4251A6_S3_L002_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6604ORPK/",
"accession": "IGVFFI6604ORPK",
"aliases": [
"harinder-singh:donor1_Bcell_multiome_ATAC_NGS_day5_6_L001_R2"
],
"content_type": "reads",
"controlled_access": true,
"creation_timestamp": "2025-03-04T22:15:05.779747+00:00",
"file_format": "fastq",
"file_size": 2205742990,
"href": "/sequence-files/IGVFFI6604ORPK/@@download/IGVFFI6604ORPK.fastq.gz",
"md5sum": "da8e64e34d3f623573a1a24555c6280c",
"s3_uri": "s3://igvf-restricted-files/2025/03/04/34bf9190-93dd-4a78-86d8-85164676606e/IGVFFI6604ORPK.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008637/",
"status": "released",
"term_name": "Illumina NovaSeq 6000"
},
"status": "preview",
"submitted_file_name": "/ix/djishnu/peasena/primary_multiome/donor1_upmc/fastqs/scATAC/NP002_03_120222_Singh_Multiome_scATAC_remade_SIN4251A6_S3_L001_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3965FIQM/",
"accession": "IGVFFI3965FIQM",
"aliases": [
"harinder-singh:donor1_Bcell_multiome_ATAC_NGS_day5_6_L002_R3"
],
"content_type": "reads",
"controlled_access": true,
"creation_timestamp": "2025-03-04T22:27:11.298438+00:00",
"file_format": "fastq",
"file_size": 4040995104,
"href": "/sequence-files/IGVFFI3965FIQM/@@download/IGVFFI3965FIQM.fastq.gz",
"md5sum": "1380a351cb40aafe6f3eda48ad1d0617",
"s3_uri": "s3://igvf-restricted-files/2025/03/04/b63d5d5b-efcb-4b21-96b4-64eee8c28f5a/IGVFFI3965FIQM.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008637/",
"status": "released",
"term_name": "Illumina NovaSeq 6000"
},
"status": "preview",
"submitted_file_name": "/ix/djishnu/peasena/primary_multiome/donor1_upmc/fastqs/scATAC/NP002_03_120222_Singh_Multiome_scATAC_remade_SIN4251A6_S3_L002_R3_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9027QUQE/",
"accession": "IGVFFI9027QUQE",
"aliases": [
"harinder-singh:donor1_Bcell_multiome_ATAC_NGS_day5_6_L002_R1"
],
"content_type": "reads",
"controlled_access": true,
"creation_timestamp": "2025-03-04T22:25:56.790218+00:00",
"file_format": "fastq",
"file_size": 4115274150,
"href": "/sequence-files/IGVFFI9027QUQE/@@download/IGVFFI9027QUQE.fastq.gz",
"md5sum": "f81a88fc13a1de9052d28f6f0e0b6727",
"s3_uri": "s3://igvf-restricted-files/2025/03/04/e3cea84d-11fd-40a0-8571-763e0e8f6212/IGVFFI9027QUQE.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008637/",
"status": "released",
"term_name": "Illumina NovaSeq 6000"
},
"status": "preview",
"submitted_file_name": "/ix/djishnu/peasena/primary_multiome/donor1_upmc/fastqs/scATAC/NP002_03_120222_Singh_Multiome_scATAC_remade_SIN4251A6_S3_L002_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0747UFCR/",
"accession": "IGVFFI0747UFCR",
"aliases": [
"harinder-singh:donor1_Bcell_multiome_ATAC_NGS_day5_6_L002_R2"
],
"content_type": "reads",
"controlled_access": true,
"creation_timestamp": "2025-03-04T22:29:50.816573+00:00",
"file_format": "fastq",
"file_size": 2179566339,
"href": "/sequence-files/IGVFFI0747UFCR/@@download/IGVFFI0747UFCR.fastq.gz",
"md5sum": "3abff39c6b3c935dc6ec0f5edb7fd6c2",
"s3_uri": "s3://igvf-restricted-files/2025/03/04/de0a34fd-a787-4a75-b4c3-7c164ba68435/IGVFFI0747UFCR.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008637/",
"status": "released",
"term_name": "Illumina NovaSeq 6000"
},
"status": "preview",
"submitted_file_name": "/ix/djishnu/peasena/primary_multiome/donor1_upmc/fastqs/scATAC/NP002_03_120222_Singh_Multiome_scATAC_remade_SIN4251A6_S3_L002_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8715LSIG/",
"accession": "IGVFFI8715LSIG",
"aliases": [
"harinder-singh:donor1_Bcell_multiome_ATAC_NGS_day5_6_L001_R1"
],
"content_type": "reads",
"controlled_access": true,
"creation_timestamp": "2025-03-04T22:18:05.220406+00:00",
"file_format": "fastq",
"file_size": 4163860706,
"href": "/sequence-files/IGVFFI8715LSIG/@@download/IGVFFI8715LSIG.fastq.gz",
"md5sum": "2dae950db9af84f281e94ea6d49ed496",
"s3_uri": "s3://igvf-restricted-files/2025/03/04/d4c6fb4b-342b-4e60-b622-a2ffacd5056f/IGVFFI8715LSIG.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008637/",
"status": "released",
"term_name": "Illumina NovaSeq 6000"
},
"status": "preview",
"submitted_file_name": "/ix/djishnu/peasena/primary_multiome/donor1_upmc/fastqs/scATAC/NP002_03_120222_Singh_Multiome_scATAC_remade_SIN4251A6_S3_L001_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8147EQBN/",
"accession": "IGVFFI8147EQBN",
"aliases": [
"harinder-singh:donor1_Bcell_multiome_ATAC_NGS_day5_6_L001_I1"
],
"content_type": "reads",
"controlled_access": true,
"creation_timestamp": "2025-03-04T22:26:40.381303+00:00",
"file_format": "fastq",
"file_size": 883530368,
"href": "/sequence-files/IGVFFI8147EQBN/@@download/IGVFFI8147EQBN.fastq.gz",
"md5sum": "760e8cb8479f398cbae8dae62754da91",
"s3_uri": "s3://igvf-restricted-files/2025/03/04/9918fe6b-e769-4b15-882a-9a231a061688/IGVFFI8147EQBN.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008637/",
"status": "released",
"term_name": "Illumina NovaSeq 6000"
},
"status": "preview",
"submitted_file_name": "/ix/djishnu/peasena/primary_multiome/donor1_upmc/fastqs/scATAC/NP002_03_120222_Singh_Multiome_scATAC_remade_SIN4251A6_S3_L001_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4365QGIG/",
"accession": "IGVFFI4365QGIG",
"aliases": [
"harinder-singh:donor1_Bcell_multiome_ATAC_NGS_day5_6_L001_R3"
],
"content_type": "reads",
"controlled_access": true,
"creation_timestamp": "2025-03-04T22:14:17.890197+00:00",
"file_format": "fastq",
"file_size": 4088831229,
"href": "/sequence-files/IGVFFI4365QGIG/@@download/IGVFFI4365QGIG.fastq.gz",
"md5sum": "c374503822f2a09a094c70950fd6df0b",
"s3_uri": "s3://igvf-restricted-files/2025/03/04/97f8e777-c9a3-4d47-a4be-3239d5a75b40/IGVFFI4365QGIG.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008637/",
"status": "released",
"term_name": "Illumina NovaSeq 6000"
},
"status": "preview",
"submitted_file_name": "/ix/djishnu/peasena/primary_multiome/donor1_upmc/fastqs/scATAC/NP002_03_120222_Singh_Multiome_scATAC_remade_SIN4251A6_S3_L001_R3_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI8567RFOG/",
"accession": "IGVFFI8567RFOG",
"aliases": [
"harinder-singh:donor1_Bcell_multiome_ATAC_NGS_day5_6_L002_atac_seqspec"
],
"content_type": "seqspec",
"creation_timestamp": "2025-04-23T20:09:26.809434+00:00",
"file_format": "yaml",
"file_size": 1480,
"href": "/configuration-files/IGVFFI8567RFOG/@@download/IGVFFI8567RFOG.yaml.gz",
"md5sum": "50a1453907fb4817efc787c30f67bad2",
"s3_uri": "s3://igvf-files/2025/04/23/4cac5268-0328-496d-a975-1f6e62786a85/IGVFFI8567RFOG.yaml.gz",
"status": "in progress",
"submitted_file_name": "/media/RAIDArray/Nick/library/seqspec_files/donor1_Bcell_multiome_ATAC_NGS_day5_6_L002_atac_seqspec.yaml.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI8385GOSF/",
"accession": "IGVFFI8385GOSF",
"aliases": [
"harinder-singh:donor1_Bcell_multiome_ATAC_NGS_day5_6_L001_atac_seqspec"
],
"content_type": "seqspec",
"creation_timestamp": "2025-04-23T20:09:43.722778+00:00",
"file_format": "yaml",
"file_size": 1477,
"href": "/configuration-files/IGVFFI8385GOSF/@@download/IGVFFI8385GOSF.yaml.gz",
"md5sum": "d91c06e14ae1495b1792dc11b7b5b5e1",
"s3_uri": "s3://igvf-files/2025/04/23/1bbf8eb4-5172-493c-8eb0-7c03ca81dd60/IGVFFI8385GOSF.yaml.gz",
"status": "in progress",
"submitted_file_name": "/media/RAIDArray/Nick/library/seqspec_files/donor1_Bcell_multiome_ATAC_NGS_day5_6_L001_atac_seqspec.yaml.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS6517LKCX/",
"/analysis-sets/IGVFDS9046UDPN/"
],
"lab": {
"@id": "/labs/harinder-singh/",
"title": "Harinder Singh, University of Pittsburgh"
},
"multiome_size": 2,
"onlist_files": [
"/tabular-files/IGVFFI7587TJLC/"
],
"onlist_method": "no combination",
"preferred_assay_title": "10x multiome",
"protocols": [
"https://www.protocols.io/file/rv9ucg3if.pdf"
],
"related_multiome_datasets": [
{
"@id": "/measurement-sets/IGVFDS8419ZMNL/",
"accession": "IGVFDS8419ZMNL",
"status": "preview"
}
],
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM1056LJKY/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM1056LJKY",
"aliases": [
"harinder-singh:D56_Bcells_don1_pitt_multiome"
],
"classifications": [
"differentiated cell specimen"
],
"institutional_certificates": [
{
"@id": "/institutional-certificates/4786e123-f40d-4b08-aa06-b5f35e9cc453/",
"certificate_identifier": "IP108-01",
"controlled_access": true,
"data_use_limitation": "HMB",
"status": "in progress"
}
],
"sample_terms": [
{
"@id": "/sample-terms/CL_0000236/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"status": "released",
"summary": "B cell",
"term_name": "B cell"
}
],
"status": "preview",
"summary": "Homo sapiens (male) B differentiated cell specimen induced to plasmablast for 6 days",
"targeted_sample_term": {
"@id": "/sample-terms/CL_0000980/",
"status": "released",
"term_name": "plasmablast"
},
"taxa": "Homo sapiens"
}
],
"schema_version": "26",
"status": "preview",
"strand_specificity": "5 prime to 3 prime",
"submitted_by": {
"@id": "/users/d2668d67-5e6f-49e8-82ca-7bb12229f892/",
"title": "Nicholas Pease"
},
"submitted_files_timestamp": "2025-03-04T22:13:45.949022+00:00",
"summary": "single-nucleus ATAC-seq (10x multiome)",
"uuid": "5e9bd8bb-aea4-485c-a0f9-723f3f888c83"
}