{
"@context": "/terms/",
"@id": "/analysis-sets/IGVFDS6790TZFT/",
"@type": [
"AnalysisSet",
"FileSet",
"Item"
],
"accession": "IGVFDS6790TZFT",
"aliases": [
"harinder-singh:multiplexed_perturbation_scRNAseq_20240212_cellranger_analysis_set"
],
"assay_titles": [
"scRNA-seq"
],
"audit": {
"INTERNAL_ACTION": [
{
"category": "mismatched status",
"detail": "Preview matrix file [IGVFFI3987VJYL](/matrix-files/IGVFFI3987VJYL/) has in progress subobject reference file [IGVFFI3944QOJF](/reference-files/IGVFFI3944QOJF/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/matrix-files/IGVFFI3987VJYL/"
},
{
"category": "missing demultiplexed sample",
"detail": "Analysis set [IGVFDS6790TZFT](/analysis-sets/IGVFDS6790TZFT/) has `input_file_sets` with multiplexed samples: [IGVFSM5472KWSO](/multiplexed-samples/IGVFSM5472KWSO/) 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/IGVFDS6790TZFT/"
}
]
},
"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": "2025-04-02T12:08:53.538440+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/IGVFFI3987VJYL/",
"accession": "IGVFFI3987VJYL",
"aliases": [
"harinder-singh:multiplexed_perturbation_scRNAseq_20240212_merged_demux_mtx"
],
"content_type": "sparse gene count matrix",
"creation_timestamp": "2025-04-02T19:42:18.982716+00:00",
"derived_from": [
"/tabular-files/IGVFFI5389DBIZ/",
"/sequence-files/IGVFFI7051LXQP/",
"/sequence-files/IGVFFI5054SLPH/",
"/sequence-files/IGVFFI5866KFBU/",
"/sequence-files/IGVFFI3786VRMJ/",
"/sequence-files/IGVFFI5911IRSC/",
"/sequence-files/IGVFFI1865PQVY/",
"/sequence-files/IGVFFI9427QGKM/",
"/sequence-files/IGVFFI8264NORL/",
"/sequence-files/IGVFFI7161VXYB/",
"/sequence-files/IGVFFI3475FKDW/",
"/sequence-files/IGVFFI7189BROY/",
"/sequence-files/IGVFFI3069IUKG/",
"/sequence-files/IGVFFI2380OHVF/",
"/sequence-files/IGVFFI0785EVIF/",
"/sequence-files/IGVFFI4842KHWR/",
"/sequence-files/IGVFFI6217HHCQ/",
"/sequence-files/IGVFFI5293ERQT/",
"/sequence-files/IGVFFI4869SUWE/",
"/sequence-files/IGVFFI1045UARS/",
"/sequence-files/IGVFFI8402CXCB/",
"/sequence-files/IGVFFI8691TPYO/",
"/sequence-files/IGVFFI9612KLAX/",
"/sequence-files/IGVFFI5739WHOD/",
"/sequence-files/IGVFFI6046HGLQ/",
"/sequence-files/IGVFFI3984UWRK/",
"/sequence-files/IGVFFI8163BHER/",
"/sequence-files/IGVFFI9553KWLN/",
"/sequence-files/IGVFFI8250YZXI/",
"/sequence-files/IGVFFI8093UBWK/",
"/sequence-files/IGVFFI2049ZZFE/",
"/sequence-files/IGVFFI9129HDQV/",
"/sequence-files/IGVFFI0829YKTW/",
"/sequence-files/IGVFFI4841RJZZ/",
"/sequence-files/IGVFFI9893FNOZ/",
"/sequence-files/IGVFFI8250VJDT/",
"/sequence-files/IGVFFI1495LZSW/",
"/sequence-files/IGVFFI4380WYZL/",
"/sequence-files/IGVFFI7509YKFB/",
"/sequence-files/IGVFFI6733RRDC/",
"/sequence-files/IGVFFI1968HTFI/",
"/sequence-files/IGVFFI5719RJDH/",
"/sequence-files/IGVFFI5757BBWU/",
"/sequence-files/IGVFFI8409DDJP/",
"/sequence-files/IGVFFI6380RLVG/",
"/sequence-files/IGVFFI4177SILN/",
"/sequence-files/IGVFFI7935BJNA/",
"/sequence-files/IGVFFI9810YLQA/",
"/sequence-files/IGVFFI2701UBNX/",
"/sequence-files/IGVFFI7826EJET/",
"/sequence-files/IGVFFI0274FVLO/",
"/sequence-files/IGVFFI0965VIXG/",
"/sequence-files/IGVFFI1765BOZQ/",
"/sequence-files/IGVFFI8512JQZI/",
"/sequence-files/IGVFFI6184LOTJ/",
"/sequence-files/IGVFFI0712MNBI/",
"/sequence-files/IGVFFI0707UJHE/",
"/sequence-files/IGVFFI3197MWIE/",
"/sequence-files/IGVFFI0335OFSR/",
"/sequence-files/IGVFFI7711XHDM/",
"/sequence-files/IGVFFI9859PQKG/",
"/sequence-files/IGVFFI9714SEEH/",
"/sequence-files/IGVFFI0022ARLY/",
"/sequence-files/IGVFFI6639HISK/",
"/sequence-files/IGVFFI4703EAAB/"
],
"file_format": "h5ad",
"file_size": 1176916500,
"href": "/matrix-files/IGVFFI3987VJYL/@@download/IGVFFI3987VJYL.h5ad",
"md5sum": "397256138ab91fe398dc900d6b2b3b84",
"s3_uri": "s3://igvf-files/2025/04/02/71b603e7-5e28-4762-97ae-2d24d32bccac/IGVFFI3987VJYL.h5ad",
"status": "preview",
"submitted_file_name": "/media/RAIDArray/Nick/20240206_PerturbSeq_Exp2/h5_files/tf_perturbseq_rep2_post_cellranger.h5ad",
"upload_status": "validated"
}
],
"functional_assay_mechanisms": [],
"input_file_sets": [
{
"@id": "/measurement-sets/IGVFDS5867EPVA/",
"accession": "IGVFDS5867EPVA",
"aliases": [
"harinder-singh:multiplexed_perturbation_scRNAseq_20240212_measurement"
],
"file_set_type": "experimental data",
"status": "preview"
},
{
"@id": "/auxiliary-sets/IGVFDS8802CHOK/",
"accession": "IGVFDS8802CHOK",
"aliases": [
"harinder-singh:multiplexed_perturbation_scRNAseq_20240212_HTO"
],
"file_set_type": "cell hashing barcode sequencing",
"status": "preview"
},
{
"@id": "/curated-sets/IGVFDS2466PXPD/",
"accession": "IGVFDS2466PXPD",
"aliases": [
"harinder-singh:multiplexed_perturbation_scRNAseq_HTO_barcode_map_set"
],
"file_set_type": "barcodes",
"status": "preview"
}
],
"input_for": [
"/analysis-sets/IGVFDS7845HWEA/"
],
"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/IGVFSM5472KWSO/",
"@type": [
"MultiplexedSample",
"Sample",
"Item"
],
"accession": "IGVFSM5472KWSO",
"aliases": [
"harinder-singh:multiplexed_perturbation_scRNAseq_20240212"
],
"classifications": [
"differentiated cell specimen",
"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 4 days; Homo sapiens (male) B differentiated cell specimen induced to plasmablast for 6 days; ... and 12 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": "2025-04-02T19:42:18.982716+00:00",
"summary": "scRNA-seq: sparse gene count matrix",
"uuid": "52c41694-d125-4f72-8916-3c0acc77ad8e",
"workflows": [
{
"@id": "/workflows/IGVFWF0081UKFO/",
"accession": "IGVFWF0081UKFO",
"name": "Singh Perturbation Single Cell RNA-seq Workflow",
"status": "in progress",
"uniform_pipeline": false
}
]
}