{
"@context": "/terms/",
"@id": "/analysis-sets/IGVFDS9167HYTZ/",
"@type": [
"AnalysisSet",
"FileSet",
"Item"
],
"accession": "IGVFDS9167HYTZ",
"aliases": [
"harinder-singh:Bcells_don1_scRNAseq_measurement_analysis_set"
],
"assay_titles": [
"scRNA-seq"
],
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing demultiplexed sample",
"detail": "Analysis set [IGVFDS9167HYTZ](/analysis-sets/IGVFDS9167HYTZ/) has `input_file_sets` with multiplexed samples: [IGVFSM8130GPCI](/multiplexed-samples/IGVFSM8130GPCI/) but no `demultiplexed_sample`. Analysis sets with multiplexed samples are expected to specify a demultiplexed sample.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_analysis_set_multiplexed_samples",
"path": "/analysis-sets/IGVFDS9167HYTZ/"
},
{
"category": "mismatched status",
"detail": "Preview matrix file [IGVFFI4444FIKL](/matrix-files/IGVFFI4444FIKL/) has in progress subobject reference file [IGVFFI5429KKCK](/reference-files/IGVFFI5429KKCK/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/matrix-files/IGVFFI4444FIKL/"
}
]
},
"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": "2025-01-09T20:05:24.280372+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/IGVFFI4444FIKL/",
"accession": "IGVFFI4444FIKL",
"aliases": [
"harinder-singh:Bcells_don1_scRNAseq_filtered_feature_barcode_mtx"
],
"content_type": "filtered feature barcode matrix",
"creation_timestamp": "2025-01-09T20:16:29.544222+00:00",
"derived_from": [
"/tabular-files/IGVFFI3895TBOX/",
"/sequence-files/IGVFFI4669PAEC/",
"/sequence-files/IGVFFI4303LQSC/",
"/sequence-files/IGVFFI5699IPNL/",
"/sequence-files/IGVFFI6844VZPJ/",
"/sequence-files/IGVFFI7785ZSYW/",
"/sequence-files/IGVFFI5049IWDT/",
"/sequence-files/IGVFFI8595LDID/",
"/sequence-files/IGVFFI2926OSLO/",
"/sequence-files/IGVFFI2547BHED/",
"/sequence-files/IGVFFI8232MDFK/",
"/sequence-files/IGVFFI0060OFIG/",
"/sequence-files/IGVFFI9889JNNL/",
"/sequence-files/IGVFFI0157FEEA/",
"/sequence-files/IGVFFI6197LEMJ/",
"/sequence-files/IGVFFI0060MPDD/",
"/sequence-files/IGVFFI4037CSAI/"
],
"file_format": "hdf5",
"file_size": 158261177,
"href": "/matrix-files/IGVFFI4444FIKL/@@download/IGVFFI4444FIKL.h5",
"md5sum": "3d5b6c7fa63bcd2e4ff6be8bc883b7c9",
"s3_uri": "s3://igvf-files/2025/01/09/3d11c183-65c5-4257-a564-cbf0d21e79a4/IGVFFI4444FIKL.h5",
"status": "preview",
"submitted_file_name": "/ix/djishnu/Common_Folder/Pease_Data/scRNA_220830/count/sample_filtered_feature_bc_matrix.h5",
"upload_status": "validated"
}
],
"functional_assay_mechanisms": [],
"input_file_sets": [
{
"@id": "/measurement-sets/IGVFDS2610IANK/",
"accession": "IGVFDS2610IANK",
"aliases": [
"harinder-singh:Bcells_don1_scRNAseq_measurement"
],
"file_set_type": "experimental data",
"status": "preview"
},
{
"@id": "/curated-sets/IGVFDS2284OEMC/",
"accession": "IGVFDS2284OEMC",
"aliases": [
"harinder-singh:multiplexed_scRNAseq_don1_r1_HTO_barcode_map"
],
"file_set_type": "barcodes",
"status": "preview"
},
{
"@id": "/auxiliary-sets/IGVFDS6876DFJK/",
"accession": "IGVFDS6876DFJK",
"aliases": [
"harinder-singh:multiplexed_scRNAseq_don1_r1_HTO"
],
"file_set_type": "cell hashing barcode sequencing",
"status": "preview"
}
],
"input_for": [
"/analysis-sets/IGVFDS3787XLRV/"
],
"lab": {
"@id": "/labs/harinder-singh/",
"title": "Harinder Singh, University of Pittsburgh"
},
"protocols": [
"https://www.protocols.io/view/preparation-of-b-cells-for-scrnaseq-n92ld8e1nv5b/v1"
],
"sample_summary": "Homo sapiens multiplexed sample of B cell",
"samples": [
{
"@id": "/multiplexed-samples/IGVFSM8130GPCI/",
"@type": [
"MultiplexedSample",
"Sample",
"Item"
],
"accession": "IGVFSM8130GPCI",
"aliases": [
"harinder-singh:multiplexed_scRNAseq_don1_r1"
],
"classifications": [
"differentiated cell specimen",
"primary cell",
"multiplexed sample"
],
"disease_terms": [],
"institutional_certificates": [
{
"@id": "/institutional-certificates/4786e123-f40d-4b08-aa06-b5f35e9cc453/",
"certificate_identifier": "IP108-01",
"controlled_access": true,
"data_use_limitation": "HMB",
"status": "in progress"
}
],
"modifications": [],
"sample_terms": [
{
"@id": "/sample-terms/CL_0000236/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"status": "released",
"summary": "B cell",
"term_name": "B cell"
}
],
"status": "preview",
"summary": "multiplexed sample: Homo sapiens (male) B differentiated cell specimen induced to plasmablast for 2 days; Homo sapiens (male) B differentiated cell specimen induced to plasmablast for 6 days; ... and 2 more samples",
"taxa": "Homo sapiens",
"treatments": []
}
],
"schema_version": "9",
"status": "preview",
"submitted_by": {
"@id": "/users/d2668d67-5e6f-49e8-82ca-7bb12229f892/",
"title": "Nicholas Pease"
},
"submitted_files_timestamp": "2025-01-09T20:16:29.544222+00:00",
"summary": "scRNA-seq: filtered feature barcode matrix",
"uuid": "fe3918c4-fadf-4e29-9efc-ee9957c49ab2",
"workflows": [
{
"@id": "/workflows/IGVFWF8690BLTY/",
"accession": "IGVFWF8690BLTY",
"name": "Singh Single Cell RNA-seq Workflow",
"status": "in progress",
"uniform_pipeline": false
}
]
}