{
"@context": "/terms/",
"@id": "/analysis-sets/IGVFDS4340KVZI/",
"@type": [
"AnalysisSet",
"FileSet",
"Item"
],
"accession": "IGVFDS4340KVZI",
"aliases": [
"harinder-singh:Bcells_don1_pitt_multiome_day012_analysis_set"
],
"assay_titles": [
"10x multiome"
],
"audit": {
"INTERNAL_ACTION": [
{
"category": "mismatched status",
"detail": "Preview matrix file [IGVFFI6053CXKY](/matrix-files/IGVFFI6053CXKY/) has in progress subobject reference file [IGVFFI0493XRYZ](/reference-files/IGVFFI0493XRYZ/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/matrix-files/IGVFFI6053CXKY/"
}
]
},
"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": "2025-04-01T14:49:59.549855+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"
}
],
"file_set_type": "intermediate analysis",
"files": [
{
"@id": "/matrix-files/IGVFFI6053CXKY/",
"accession": "IGVFFI6053CXKY",
"aliases": [
"harinder-singh:Bcells_don1_pitt_multiome_day012_gex_molecule_info_mtx"
],
"content_type": "raw feature barcode matrix",
"creation_timestamp": "2025-04-02T02:03:12.207002+00:00",
"derived_from": [
"/sequence-files/IGVFFI0633YPSK/",
"/sequence-files/IGVFFI3557HDSC/",
"/sequence-files/IGVFFI8208VRGS/",
"/sequence-files/IGVFFI4844LRLJ/",
"/sequence-files/IGVFFI4355VZKC/",
"/sequence-files/IGVFFI3653OYSB/",
"/sequence-files/IGVFFI0486KRGW/",
"/sequence-files/IGVFFI2989ICSG/",
"/sequence-files/IGVFFI3433YEFI/",
"/sequence-files/IGVFFI3739JOEC/",
"/sequence-files/IGVFFI9249PWWE/",
"/sequence-files/IGVFFI8641BMYV/",
"/sequence-files/IGVFFI5849BWNL/",
"/sequence-files/IGVFFI3482VZAG/",
"/sequence-files/IGVFFI4080SDQJ/",
"/sequence-files/IGVFFI7615HIGI/",
"/sequence-files/IGVFFI7400ROID/",
"/sequence-files/IGVFFI3708MZMR/",
"/sequence-files/IGVFFI3333MNRU/",
"/sequence-files/IGVFFI3613ESHP/",
"/sequence-files/IGVFFI9945HRIU/",
"/sequence-files/IGVFFI9998MEBG/",
"/sequence-files/IGVFFI2105ICHL/",
"/sequence-files/IGVFFI2337CWXJ/"
],
"file_format": "hdf5",
"file_size": 392568814,
"href": "/matrix-files/IGVFFI6053CXKY/@@download/IGVFFI6053CXKY.h5",
"md5sum": "1f2c1bda4079154b978c00a6c9982d8f",
"s3_uri": "s3://igvf-files/2025/04/02/ed335caa-d768-4965-ae98-96d4b4cc67f0/IGVFFI6053CXKY.h5",
"status": "preview",
"submitted_file_name": "/ix/djishnu/Common_Folder/Jingyu_Data/multiome_1st_donor_UPMC_day0_2/outs/gex_molecule_info.h5",
"upload_status": "validated"
},
{
"@id": "/tabular-files/IGVFFI4235BPMB/",
"accession": "IGVFFI4235BPMB",
"aliases": [
"harinder-singh:Bcells_don1_pitt_multiome_day012_atac_fragments"
],
"content_type": "fragments",
"controlled_access": true,
"creation_timestamp": "2025-04-02T02:13:55.840289+00:00",
"derived_from": [
"/sequence-files/IGVFFI0633YPSK/",
"/sequence-files/IGVFFI3557HDSC/",
"/sequence-files/IGVFFI8208VRGS/",
"/sequence-files/IGVFFI4844LRLJ/",
"/sequence-files/IGVFFI4355VZKC/",
"/sequence-files/IGVFFI3653OYSB/",
"/sequence-files/IGVFFI0486KRGW/",
"/sequence-files/IGVFFI2989ICSG/",
"/sequence-files/IGVFFI3433YEFI/",
"/sequence-files/IGVFFI3739JOEC/",
"/sequence-files/IGVFFI9249PWWE/",
"/sequence-files/IGVFFI8641BMYV/",
"/sequence-files/IGVFFI5849BWNL/",
"/sequence-files/IGVFFI3482VZAG/",
"/sequence-files/IGVFFI4080SDQJ/",
"/sequence-files/IGVFFI7615HIGI/",
"/sequence-files/IGVFFI7400ROID/",
"/sequence-files/IGVFFI3708MZMR/",
"/sequence-files/IGVFFI3333MNRU/",
"/sequence-files/IGVFFI3613ESHP/",
"/sequence-files/IGVFFI9945HRIU/",
"/sequence-files/IGVFFI9998MEBG/",
"/sequence-files/IGVFFI2105ICHL/",
"/sequence-files/IGVFFI2337CWXJ/"
],
"file_format": "tsv",
"file_size": 1830302595,
"href": "/tabular-files/IGVFFI4235BPMB/@@download/IGVFFI4235BPMB.tsv.gz",
"md5sum": "55db4df2dee67fc5dc7f2d2817fb5a1e",
"s3_uri": "s3://igvf-restricted-files/2025/04/02/4d8940b6-0e8c-4370-a693-3d5204e9675e/IGVFFI4235BPMB.tsv.gz",
"status": "preview",
"submitted_file_name": "/ix/djishnu/Common_Folder/Jingyu_Data/multiome_1st_donor_UPMC_day0_2/outs/atac_fragments.tsv.gz",
"upload_status": "validated"
},
{
"@id": "/tabular-files/IGVFFI9078MASJ/",
"accession": "IGVFFI9078MASJ",
"aliases": [
"harinder-singh:Bcells_don1_pitt_multiome_day012_per_barcode_metrics"
],
"content_type": "barcode to element mapping",
"controlled_access": true,
"creation_timestamp": "2025-04-02T02:15:36.578062+00:00",
"derived_from": [
"/sequence-files/IGVFFI0633YPSK/",
"/sequence-files/IGVFFI3557HDSC/",
"/sequence-files/IGVFFI8208VRGS/",
"/sequence-files/IGVFFI4844LRLJ/",
"/sequence-files/IGVFFI4355VZKC/",
"/sequence-files/IGVFFI3653OYSB/",
"/sequence-files/IGVFFI0486KRGW/",
"/sequence-files/IGVFFI2989ICSG/",
"/sequence-files/IGVFFI3433YEFI/",
"/sequence-files/IGVFFI3739JOEC/",
"/sequence-files/IGVFFI9249PWWE/",
"/sequence-files/IGVFFI8641BMYV/",
"/sequence-files/IGVFFI5849BWNL/",
"/sequence-files/IGVFFI3482VZAG/",
"/sequence-files/IGVFFI4080SDQJ/",
"/sequence-files/IGVFFI7615HIGI/",
"/sequence-files/IGVFFI7400ROID/",
"/sequence-files/IGVFFI3708MZMR/",
"/sequence-files/IGVFFI3333MNRU/",
"/sequence-files/IGVFFI3613ESHP/",
"/sequence-files/IGVFFI9945HRIU/",
"/sequence-files/IGVFFI9998MEBG/",
"/sequence-files/IGVFFI2105ICHL/",
"/sequence-files/IGVFFI2337CWXJ/"
],
"file_format": "csv",
"file_size": 17021090,
"href": "/tabular-files/IGVFFI9078MASJ/@@download/IGVFFI9078MASJ.csv.gz",
"md5sum": "9844cea8f509bdf74186975bb4570af6",
"s3_uri": "s3://igvf-restricted-files/2025/04/02/51c9f98f-f01c-4eb6-9dfb-ac42a4ad389c/IGVFFI9078MASJ.csv.gz",
"status": "preview",
"submitted_file_name": "/ix/djishnu/peasena/primary_multiome/donor1_upmc/cellranger_intermediate_files/day012/per_barcode_metrics.csv.gz",
"upload_status": "validated"
}
],
"functional_assay_mechanisms": [],
"input_file_sets": [
{
"@id": "/measurement-sets/IGVFDS7859EYQR/",
"accession": "IGVFDS7859EYQR",
"aliases": [
"harinder-singh:Bcells_don1_pitt_multiome_scRNAseq_day012_measurement"
],
"file_set_type": "experimental data",
"status": "preview"
},
{
"@id": "/measurement-sets/IGVFDS4024LHFB/",
"accession": "IGVFDS4024LHFB",
"aliases": [
"harinder-singh:Bcells_don1_pitt_multiome_scATACseq_day012_measurement"
],
"file_set_type": "experimental data",
"status": "preview"
}
],
"input_for": [
"/analysis-sets/IGVFDS8424XWBB/"
],
"lab": {
"@id": "/labs/harinder-singh/",
"title": "Harinder Singh, University of Pittsburgh"
},
"protocols": [
"https://www.protocols.io/file/rv9ucg3if.pdf"
],
"sample_summary": "Homo sapiens B differentiated cell specimen induced to plasmablast, at 2 day(s) post change",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM8093SHHZ/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM8093SHHZ",
"aliases": [
"harinder-singh:D012_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 2 days",
"targeted_sample_term": {
"@id": "/sample-terms/CL_0000980/",
"status": "released",
"term_name": "plasmablast"
},
"taxa": "Homo sapiens"
}
],
"schema_version": "9",
"status": "preview",
"submitted_by": {
"@id": "/users/d2668d67-5e6f-49e8-82ca-7bb12229f892/",
"title": "Nicholas Pease"
},
"submitted_files_timestamp": "2025-04-02T02:03:12.207002+00:00",
"summary": "single-nucleus ATAC-seq (10x multiome), single-nucleus RNA sequencing assay (10x multiome)",
"uuid": "ea1acef2-8c3f-4991-bf70-ff89ff5f2964",
"workflows": [
{
"@id": "/workflows/IGVFWF8495CUNO/",
"accession": "IGVFWF8495CUNO",
"name": "Singh Single Cell Multiome Workflow",
"status": "in progress",
"uniform_pipeline": false
}
]
}