{
"@context": "/terms/",
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],
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"aliases": [
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],
"assay_titles": [
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],
"audit": {
"ERROR": [
{
"category": "unexpected input file set",
"detail": "Analysis set [IGVFDS1588TVKF](/analysis-sets/IGVFDS1588TVKF/) links to file set(s): [IGVFDS4028IRAH](/measurement-sets/IGVFDS4028IRAH/), [IGVFDS2693DPLW](/auxiliary-sets/IGVFDS2693DPLW/), [IGVFDS8810ABUD](/measurement-sets/IGVFDS8810ABUD/), [IGVFDS2143BSOH](/measurement-sets/IGVFDS2143BSOH/), [IGVFDS7986GKWR](/auxiliary-sets/IGVFDS7986GKWR/), [IGVFDS3567LQMB](/auxiliary-sets/IGVFDS3567LQMB/), [IGVFDS2612LSTD](/auxiliary-sets/IGVFDS2612LSTD/), [IGVFDS2549GCKW](/auxiliary-sets/IGVFDS2549GCKW/), [IGVFDS2600XYHD](/auxiliary-sets/IGVFDS2600XYHD/), [IGVFDS5339UNRP](/auxiliary-sets/IGVFDS5339UNRP/), [IGVFDS0657YBVN](/measurement-sets/IGVFDS0657YBVN/), [IGVFDS4262EBDF](/auxiliary-sets/IGVFDS4262EBDF/) in `input_file_sets` that are not represented in the `derived_from` of the file sets of the files in this analysis. The analysis set input files are expected to belong to the input file sets.",
"level": 60,
"level_name": "ERROR",
"name": "audit_input_file_sets_derived_from",
"path": "/analysis-sets/IGVFDS1588TVKF/"
}
],
"INTERNAL_ACTION": [
{
"category": "mismatched status",
"detail": "Preview matrix file [IGVFFI0412HTWJ](/matrix-files/IGVFFI0412HTWJ/) has in progress subobject analysis step version [4cfc022a-ff63-4d13-99f7-257a6bfe4bd7](/analysis-step-versions/4cfc022a-ff63-4d13-99f7-257a6bfe4bd7/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/matrix-files/IGVFFI0412HTWJ/"
},
{
"category": "mismatched status",
"detail": "Preview matrix file [IGVFFI8487QYZL](/matrix-files/IGVFFI8487QYZL/) has in progress subobject analysis step version [65c095ee-8330-48d0-bc03-d930326fe393](/analysis-step-versions/65c095ee-8330-48d0-bc03-d930326fe393/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/matrix-files/IGVFFI8487QYZL/"
},
{
"category": "mismatched status",
"detail": "Preview matrix file [IGVFFI9503SXXQ](/matrix-files/IGVFFI9503SXXQ/) has in progress subobject analysis step version [65c095ee-8330-48d0-bc03-d930326fe393](/analysis-step-versions/65c095ee-8330-48d0-bc03-d930326fe393/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/matrix-files/IGVFFI9503SXXQ/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing derived from",
"detail": "Analysis set [IGVFDS1588TVKF](/analysis-sets/IGVFDS1588TVKF/) links to file(s) [IGVFFI0412HTWJ](/matrix-files/IGVFFI0412HTWJ/), [IGVFFI9503SXXQ](/matrix-files/IGVFFI9503SXXQ/), [IGVFFI8487QYZL](/matrix-files/IGVFFI8487QYZL/) that have no `derived_from`. Files in an analysis set are expected to be derived from other files.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_input_file_sets_derived_from",
"path": "/analysis-sets/IGVFDS1588TVKF/"
}
]
},
"award": {
"@id": "/awards/HG011996/",
"component": "functional characterization",
"contact_pi": {
"@id": "/users/95d84f03-8ce0-489c-a755-f33ced139c5d/",
"title": "Gary Hon"
},
"title": "Multiscale functional characterization of genomic variation in human developmental disorders"
},
"control_for": [],
"creation_timestamp": "2024-12-04T20:01:58.796610+00:00",
"donors": [
{
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"accession": "IGVFDO1756PPKO",
"aliases": [
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],
"sex": "male",
"status": "released",
"taxa": "Homo sapiens"
}
],
"file_set_type": "principal analysis",
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{
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"accession": "IGVFFI0412HTWJ",
"aliases": [
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],
"content_type": "sparse gene count matrix",
"creation_timestamp": "2024-12-17T22:34:40.183863+00:00",
"file_format": "h5ad",
"file_size": 17405080439,
"href": "/matrix-files/IGVFFI0412HTWJ/@@download/IGVFFI0412HTWJ.h5ad",
"s3_uri": "s3://igvf-files/2024/12/17/d04c0f93-9ce3-4c6f-a28f-e24cfd3c25ac/IGVFFI0412HTWJ.h5ad",
"status": "preview",
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},
{
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"aliases": [
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],
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"creation_timestamp": "2024-12-17T23:39:58.712141+00:00",
"file_format": "hdf5",
"file_size": 508318738,
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"status": "preview",
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"upload_status": "validated"
},
{
"@id": "/matrix-files/IGVFFI8487QYZL/",
"accession": "IGVFFI8487QYZL",
"aliases": [
"gary-hon:WTC11_TF_Perturb_Seq_Pilot_NPC_Lenti_PrimaryAnalysis_pkl"
],
"content_type": "raw feature barcode matrix",
"creation_timestamp": "2024-12-17T23:40:13.934021+00:00",
"file_format": "pkl",
"file_size": 540005995,
"href": "/matrix-files/IGVFFI8487QYZL/@@download/IGVFFI8487QYZLpkl",
"s3_uri": "s3://igvf-files/2024/12/17/45e4e140-eb79-4938-aeca-a0dd81528ecf/IGVFFI8487QYZLpkl",
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/s215194/Single_Cell/TF_perturb_seq/_pipeline_reporcessing/_combined_npc/aggr_dataframe/aggr_combined_df_full.pkl",
"upload_status": "validated"
}
],
"functional_assay_mechanisms": [],
"input_file_sets": [
{
"@id": "/measurement-sets/IGVFDS2143BSOH/",
"accession": "IGVFDS2143BSOH",
"aliases": [
"gary-hon:TF_Perturb_Seq_Pilot_Lenti_NPC_LW281"
],
"file_set_type": "experimental data",
"status": "preview"
},
{
"@id": "/auxiliary-sets/IGVFDS2612LSTD/",
"accession": "IGVFDS2612LSTD",
"aliases": [
"gary-hon:TF_Perturb_Seq_Pilot_Lenti_NPC_sgRNA_LW281"
],
"file_set_type": "gRNA sequencing",
"status": "preview"
},
{
"@id": "/auxiliary-sets/IGVFDS2549GCKW/",
"accession": "IGVFDS2549GCKW",
"aliases": [
"gary-hon:TF_Perturb_Seq_Pilot_Lenti_NPC_HTO_LW281"
],
"file_set_type": "cell hashing barcode sequencing",
"status": "preview"
},
{
"@id": "/measurement-sets/IGVFDS8810ABUD/",
"accession": "IGVFDS8810ABUD",
"aliases": [
"gary-hon:TF_Perturb_Seq_Pilot_Lenti_NPC_LW282"
],
"file_set_type": "experimental data",
"status": "preview"
},
{
"@id": "/auxiliary-sets/IGVFDS7986GKWR/",
"accession": "IGVFDS7986GKWR",
"aliases": [
"gary-hon:TF_Perturb_Seq_Pilot_Lenti_NPC_sgRNA_LW282"
],
"file_set_type": "gRNA sequencing",
"status": "preview"
},
{
"@id": "/auxiliary-sets/IGVFDS3567LQMB/",
"accession": "IGVFDS3567LQMB",
"aliases": [
"gary-hon:TF_Perturb_Seq_Pilot_Lenti_NPC_HTO_LW282"
],
"file_set_type": "cell hashing barcode sequencing",
"status": "preview"
},
{
"@id": "/measurement-sets/IGVFDS4028IRAH/",
"accession": "IGVFDS4028IRAH",
"aliases": [
"gary-hon:TF_Perturb_Seq_Pilot_Lenti_NPC_LW283"
],
"file_set_type": "experimental data",
"status": "preview"
},
{
"@id": "/auxiliary-sets/IGVFDS4262EBDF/",
"accession": "IGVFDS4262EBDF",
"aliases": [
"gary-hon:TF_Perturb_Seq_Pilot_Lenti_NPC_sgRNA_LW283"
],
"file_set_type": "gRNA sequencing",
"status": "preview"
},
{
"@id": "/auxiliary-sets/IGVFDS2600XYHD/",
"accession": "IGVFDS2600XYHD",
"aliases": [
"gary-hon:TF_Perturb_Seq_Pilot_Lenti_NPC_HTO_LW283"
],
"file_set_type": "cell hashing barcode sequencing",
"status": "preview"
},
{
"@id": "/measurement-sets/IGVFDS0657YBVN/",
"accession": "IGVFDS0657YBVN",
"aliases": [
"gary-hon:TF_Perturb_Seq_Pilot_Lenti_NPC_LW284"
],
"file_set_type": "experimental data",
"status": "preview"
},
{
"@id": "/auxiliary-sets/IGVFDS5339UNRP/",
"accession": "IGVFDS5339UNRP",
"aliases": [
"gary-hon:TF_Perturb_Seq_Pilot_Lenti_NPC_sgRNA_LW284"
],
"file_set_type": "gRNA sequencing",
"status": "preview"
},
{
"@id": "/auxiliary-sets/IGVFDS2693DPLW/",
"accession": "IGVFDS2693DPLW",
"aliases": [
"gary-hon:TF_Perturb_Seq_Pilot_Lenti_NPC_HTO_LW284"
],
"file_set_type": "cell hashing barcode sequencing",
"status": "preview"
}
],
"input_for": [],
"lab": {
"@id": "/labs/gary-hon/",
"title": "Gary Hon, UT"
},
"protocols": [
"https://www.protocols.io/view/experimental-procedures-for-tf-perturb-seq-ut-sout-denf3dbn"
],
"sample_summary": "GM25256 (WTC-11) differentiated cell specimen induced to neural stem cell, at 1 time point(s) post change, modified with CRISPR modifications, transfected with a guide library",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM0956HKRJ/",
"@type": [
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"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM0956HKRJ",
"aliases": [
"nikhil-munshi:differentited_WTC11_TF_Perturb_Seq_Pilot_NPC_Lenti_LW281"
],
"classifications": [
"differentiated cell specimen"
],
"construct_library_sets": [
"/construct-library-sets/IGVFDS2302LCEO/"
],
"modifications": [
{
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],
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"OntologyTerm",
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],
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],
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}
],
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"targeted_sample_term": {
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{
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],
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],
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],
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}
],
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{
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"@type": [
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"OntologyTerm",
"Item"
],
"aliases": [
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],
"status": "released",
"summary": "GM25256 (WTC-11)",
"term_name": "GM25256 (WTC-11)"
}
],
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},
{
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"Sample",
"Item"
],
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],
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],
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],
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],
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],
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}
],
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},
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},
{
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"Biosample",
"Sample",
"Item"
],
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"nikhil-munshi:differentited_WTC11_TF_Perturb_Seq_Pilot_NPC_Lenti_LW282"
],
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"differentiated cell specimen"
],
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],
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{
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"modality": "interference",
"status": "preview"
}
],
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{
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"@type": [
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"OntologyTerm",
"Item"
],
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],
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"summary": "GM25256 (WTC-11)",
"term_name": "GM25256 (WTC-11)"
}
],
"status": "preview",
"summary": "GM25256 (WTC-11) differentiated cell specimen induced to neural stem cell for 20 days (cellular sub pool: subpool_LW282), male, Homo sapiens modified with CRISPRi Sp-dCas9, transduced (lentivirus) with a guide library",
"targeted_sample_term": {
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"status": "preview",
"term_name": "neural stem cell"
},
"taxa": "Homo sapiens"
}
],
"schema_version": "9",
"status": "preview",
"submitted_by": {
"@id": "/users/b05645f1-2d56-4a5e-b272-4601e555a3fa/",
"title": "Mpathi Nzima"
},
"submitted_files_timestamp": "2024-12-17T22:34:40.183863+00:00",
"submitter_comment": "Differential expression was not performed due to low computational analysis power of the dataset and cell count",
"summary": "interference Perturb-seq: filtered feature barcode matrix, raw feature barcode matrix, sparse gene count matrix",
"uuid": "89c7a51d-f7f2-4c3e-ba52-036da8010898",
"workflows": [
{
"@id": "/workflows/IGVFWF0190YALU/",
"accession": "IGVFWF0190YALU",
"name": "Hon Perturb-seq Workflow",
"status": "in progress",
"uniform_pipeline": false
}
]
}