{
"@context": "/terms/",
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"@type": [
"AnalysisSet",
"FileSet",
"Item"
],
"accession": "IGVFDS9192YMGI",
"aliases": [
"gary-hon:CM_Pilot_2_PB_RNA"
],
"assay_titles": [
"Perturb-seq"
],
"audit": {
"ERROR": [
{
"category": "unexpected input file set",
"detail": "Analysis set [IGVFDS9192YMGI](/analysis-sets/IGVFDS9192YMGI/) links to file set(s): [IGVFDS1334EIHS](/measurement-sets/IGVFDS1334EIHS/), [IGVFDS2593KURF](/measurement-sets/IGVFDS2593KURF/), [IGVFDS7242KAVQ](/auxiliary-sets/IGVFDS7242KAVQ/), [IGVFDS9976WMCI](/auxiliary-sets/IGVFDS9976WMCI/), [IGVFDS7504HTXW](/auxiliary-sets/IGVFDS7504HTXW/), [IGVFDS9856AQIW](/auxiliary-sets/IGVFDS9856AQIW/), [IGVFDS8202GWXE](/auxiliary-sets/IGVFDS8202GWXE/), [IGVFDS1726RJYG](/auxiliary-sets/IGVFDS1726RJYG/), [IGVFDS0588CNDW](/auxiliary-sets/IGVFDS0588CNDW/), [IGVFDS5986XHYV](/auxiliary-sets/IGVFDS5986XHYV/), [IGVFDS0019ZVVN](/auxiliary-sets/IGVFDS0019ZVVN/), [IGVFDS8705MRYI](/measurement-sets/IGVFDS8705MRYI/), [IGVFDS0890CUXC](/measurement-sets/IGVFDS0890CUXC/), [IGVFDS2406OSFC](/auxiliary-sets/IGVFDS2406OSFC/), [IGVFDS9005AVSB](/measurement-sets/IGVFDS9005AVSB/), [IGVFDS3212YIVB](/auxiliary-sets/IGVFDS3212YIVB/), [IGVFDS6402AFPQ](/auxiliary-sets/IGVFDS6402AFPQ/), [IGVFDS7019VPKV](/auxiliary-sets/IGVFDS7019VPKV/), [IGVFDS4323LXLZ](/measurement-sets/IGVFDS4323LXLZ/), [IGVFDS8701ERXN](/measurement-sets/IGVFDS8701ERXN/), [IGVFDS9925GTMC](/auxiliary-sets/IGVFDS9925GTMC/), [IGVFDS1663ZHVE](/measurement-sets/IGVFDS1663ZHVE/), [IGVFDS2333GHSM](/auxiliary-sets/IGVFDS2333GHSM/), [IGVFDS2136RFQE](/auxiliary-sets/IGVFDS2136RFQE/) 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/IGVFDS9192YMGI/"
}
],
"INTERNAL_ACTION": [
{
"category": "mismatched status",
"detail": "Preview matrix file [IGVFFI8111GDGE](/matrix-files/IGVFFI8111GDGE/) 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/IGVFFI8111GDGE/"
},
{
"category": "mismatched status",
"detail": "Preview matrix file [IGVFFI7202EABO](/matrix-files/IGVFFI7202EABO/) 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/IGVFFI7202EABO/"
},
{
"category": "mismatched status",
"detail": "Preview matrix file [IGVFFI3575TVLQ](/matrix-files/IGVFFI3575TVLQ/) 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/IGVFFI3575TVLQ/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing derived from",
"detail": "Analysis set [IGVFDS9192YMGI](/analysis-sets/IGVFDS9192YMGI/) links to file(s) [IGVFFI3575TVLQ](/matrix-files/IGVFFI3575TVLQ/), [IGVFFI7202EABO](/matrix-files/IGVFFI7202EABO/), [IGVFFI8111GDGE](/matrix-files/IGVFFI8111GDGE/) 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/IGVFDS9192YMGI/"
}
]
},
"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": "2024-12-04T22:34:21.376486+00:00",
"donors": [
{
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"accession": "IGVFDO1756PPKO",
"aliases": [
"igvf:donor_of_WTC11"
],
"sex": "male",
"status": "released",
"taxa": "Homo sapiens"
}
],
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{
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"accession": "IGVFFI3575TVLQ",
"aliases": [
"gary-hon:CM_Pilot_2_PB_RNA_h5ad"
],
"content_type": "sparse gene count matrix",
"creation_timestamp": "2024-12-17T22:53:19.371480+00:00",
"file_format": "h5ad",
"file_size": 18633113988,
"href": "/matrix-files/IGVFFI3575TVLQ/@@download/IGVFFI3575TVLQ.h5ad",
"s3_uri": "s3://igvf-files/2024/12/17/96789956-ec90-425f-b452-ab0002effa79/IGVFFI3575TVLQ.h5ad",
"status": "preview",
"submitted_file_name": "/project/shared/gcrb_igvf/data/shared/CMPILOT2_scRNAseq/H5AD/V0_CM_Pilot#02_reprocessed_sgRNACells_filtered_no_embedding_filtered_full.h5ad",
"upload_status": "validated"
},
{
"@id": "/matrix-files/IGVFFI7202EABO/",
"accession": "IGVFFI7202EABO",
"aliases": [
"gary-hon:CM_Pilot_2_PB_RNA_h5"
],
"content_type": "filtered feature barcode matrix",
"creation_timestamp": "2024-12-17T23:45:01.304810+00:00",
"file_format": "hdf5",
"file_size": 782933290,
"href": "/matrix-files/IGVFFI7202EABO/@@download/IGVFFI7202EABO.h5",
"s3_uri": "s3://igvf-files/2024/12/17/d671c2d0-78d2-44d6-8b41-156628cdd2ac/IGVFFI7202EABO.h5",
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/s215194/Single_Cell/Process_scRNA_CMPILOT2/pipeline_reprocessing/_all_lanes_combined/aggr_transcriptome/CMPILOT2_MN/outs/count/filtered_feature_bc_matrix.h5",
"upload_status": "validated"
},
{
"@id": "/matrix-files/IGVFFI8111GDGE/",
"accession": "IGVFFI8111GDGE",
"aliases": [
"gary-hon:CM_Pilot_2_PB_RNA_pkl"
],
"content_type": "raw feature barcode matrix",
"creation_timestamp": "2024-12-17T23:45:29.636217+00:00",
"file_format": "pkl",
"file_size": 4528523869,
"href": "/matrix-files/IGVFFI8111GDGE/@@download/IGVFFI8111GDGEpkl",
"s3_uri": "s3://igvf-files/2024/12/17/7a50e535-953c-47b3-b741-18782b6c4aa9/IGVFFI8111GDGEpkl",
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/s215194/Single_Cell/Process_scRNA_CMPILOT2/pipeline_reprocessing/_all_lanes_combined/aggr_dataframe/aggr_combined_df_full.pkl",
"upload_status": "validated"
}
],
"functional_assay_mechanisms": [],
"input_file_sets": [
{
"@id": "/measurement-sets/IGVFDS1334EIHS/",
"accession": "IGVFDS1334EIHS",
"aliases": [
"gary-hon:CM_Pilot_2_PB_RNA_LW231"
],
"file_set_type": "experimental data",
"status": "preview"
},
{
"@id": "/auxiliary-sets/IGVFDS5986XHYV/",
"accession": "IGVFDS5986XHYV",
"aliases": [
"gary-hon:CM_Pilot_2_PB_HTO_LW231"
],
"file_set_type": "cell hashing barcode sequencing",
"status": "preview"
},
{
"@id": "/auxiliary-sets/IGVFDS7504HTXW/",
"accession": "IGVFDS7504HTXW",
"aliases": [
"gary-hon:CM_Pilot_2_PB_sgRNA_LW231"
],
"file_set_type": "gRNA sequencing",
"status": "preview"
},
{
"@id": "/measurement-sets/IGVFDS9005AVSB/",
"accession": "IGVFDS9005AVSB",
"aliases": [
"gary-hon:CM_Pilot_2_PB_RNA_LW232"
],
"file_set_type": "experimental data",
"status": "preview"
},
{
"@id": "/auxiliary-sets/IGVFDS0019ZVVN/",
"accession": "IGVFDS0019ZVVN",
"aliases": [
"gary-hon:CM_Pilot_2_PB_HTO_LW232"
],
"file_set_type": "cell hashing barcode sequencing",
"status": "preview"
},
{
"@id": "/auxiliary-sets/IGVFDS8202GWXE/",
"accession": "IGVFDS8202GWXE",
"aliases": [
"gary-hon:CM_Pilot_2_PB_sgRNA_LW232"
],
"file_set_type": "gRNA sequencing",
"status": "preview"
},
{
"@id": "/measurement-sets/IGVFDS4323LXLZ/",
"accession": "IGVFDS4323LXLZ",
"aliases": [
"gary-hon:CM_Pilot_2_PB_RNA_LW233"
],
"file_set_type": "experimental data",
"status": "preview"
},
{
"@id": "/auxiliary-sets/IGVFDS9856AQIW/",
"accession": "IGVFDS9856AQIW",
"aliases": [
"gary-hon:CM_Pilot_2_PB_HTO_LW233"
],
"file_set_type": "cell hashing barcode sequencing",
"status": "preview"
},
{
"@id": "/auxiliary-sets/IGVFDS2333GHSM/",
"accession": "IGVFDS2333GHSM",
"aliases": [
"gary-hon:CM_Pilot_2_PB_sgRNA_LW233"
],
"file_set_type": "gRNA sequencing",
"status": "preview"
},
{
"@id": "/measurement-sets/IGVFDS8705MRYI/",
"accession": "IGVFDS8705MRYI",
"aliases": [
"gary-hon:CM_Pilot_2_PB_RNA_LW234"
],
"file_set_type": "experimental data",
"status": "preview"
},
{
"@id": "/auxiliary-sets/IGVFDS0588CNDW/",
"accession": "IGVFDS0588CNDW",
"aliases": [
"gary-hon:CM_Pilot_2_PB_HTO_LW234"
],
"file_set_type": "cell hashing barcode sequencing",
"status": "preview"
},
{
"@id": "/auxiliary-sets/IGVFDS2136RFQE/",
"accession": "IGVFDS2136RFQE",
"aliases": [
"gary-hon:CM_Pilot_2_PB_sgRNA_LW234"
],
"file_set_type": "gRNA sequencing",
"status": "preview"
},
{
"@id": "/measurement-sets/IGVFDS1663ZHVE/",
"accession": "IGVFDS1663ZHVE",
"aliases": [
"gary-hon:CM_Pilot_2_PB_RNA_LW235"
],
"file_set_type": "experimental data",
"status": "preview"
},
{
"@id": "/auxiliary-sets/IGVFDS1726RJYG/",
"accession": "IGVFDS1726RJYG",
"aliases": [
"gary-hon:CM_Pilot_2_PB_HTO_LW235"
],
"file_set_type": "cell hashing barcode sequencing",
"status": "preview"
},
{
"@id": "/auxiliary-sets/IGVFDS7242KAVQ/",
"accession": "IGVFDS7242KAVQ",
"aliases": [
"gary-hon:CM_Pilot_2_PB_sgRNA_LW235"
],
"file_set_type": "gRNA sequencing",
"status": "preview"
},
{
"@id": "/measurement-sets/IGVFDS0890CUXC/",
"accession": "IGVFDS0890CUXC",
"aliases": [
"gary-hon:CM_Pilot_2_PB_RNA_LW236"
],
"file_set_type": "experimental data",
"status": "preview"
},
{
"@id": "/auxiliary-sets/IGVFDS9925GTMC/",
"accession": "IGVFDS9925GTMC",
"aliases": [
"gary-hon:CM_Pilot_2_PB_HTO_LW236"
],
"file_set_type": "cell hashing barcode sequencing",
"status": "preview"
},
{
"@id": "/auxiliary-sets/IGVFDS9976WMCI/",
"accession": "IGVFDS9976WMCI",
"aliases": [
"gary-hon:CM_Pilot_2_PB_sgRNA_LW236"
],
"file_set_type": "gRNA sequencing",
"status": "preview"
},
{
"@id": "/measurement-sets/IGVFDS2593KURF/",
"accession": "IGVFDS2593KURF",
"aliases": [
"gary-hon:CM_Pilot_2_PB_RNA_LW237"
],
"file_set_type": "experimental data",
"status": "preview"
},
{
"@id": "/auxiliary-sets/IGVFDS2406OSFC/",
"accession": "IGVFDS2406OSFC",
"aliases": [
"gary-hon:CM_Pilot_2_PB_HTO_LW237"
],
"file_set_type": "cell hashing barcode sequencing",
"status": "preview"
},
{
"@id": "/auxiliary-sets/IGVFDS3212YIVB/",
"accession": "IGVFDS3212YIVB",
"aliases": [
"gary-hon:CM_Pilot_2_PB_sgRNA_LW237"
],
"file_set_type": "gRNA sequencing",
"status": "preview"
},
{
"@id": "/measurement-sets/IGVFDS8701ERXN/",
"accession": "IGVFDS8701ERXN",
"aliases": [
"gary-hon:CM_Pilot_2_PB_RNA_LW238"
],
"file_set_type": "experimental data",
"status": "preview"
},
{
"@id": "/auxiliary-sets/IGVFDS6402AFPQ/",
"accession": "IGVFDS6402AFPQ",
"aliases": [
"gary-hon:CM_Pilot_2_PB_HTO_LW238"
],
"file_set_type": "cell hashing barcode sequencing",
"status": "preview"
},
{
"@id": "/auxiliary-sets/IGVFDS7019VPKV/",
"accession": "IGVFDS7019VPKV",
"aliases": [
"gary-hon:CM_Pilot_2_PB_sgRNA_LW238"
],
"file_set_type": "gRNA 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 cardiac muscle cell, at 1 time point(s) post change, modified with CRISPR modifications, transfected with a guide library",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM4953FLXN/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM4953FLXN",
"aliases": [
"nikhil-munshi:differentited_WTC11_CM_Pilot1_PB_LW232"
],
"classifications": [
"differentiated cell specimen"
],
"construct_library_sets": [
"/construct-library-sets/IGVFDS9629YZLO/"
],
"modifications": [
{
"@id": "/crispr-modifications/0a63b754-eca4-44aa-bbc2-fccdc6c44fb5/",
"modality": "interference",
"status": "preview"
}
],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0009747/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"aliases": [
"igvf:WTC11"
],
"status": "released",
"summary": "GM25256 (WTC-11)",
"term_name": "GM25256 (WTC-11)"
}
],
"status": "preview",
"summary": "GM25256 (WTC-11) differentiated cell specimen induced to cardiac muscle cell for 12 days (cellular sub pool: subpool_LW262), male, Homo sapiens modified with CRISPRi Sp-dCas9, transfected with a guide library",
"targeted_sample_term": {
"@id": "/sample-terms/CL_0000746/",
"status": "released",
"term_name": "cardiac muscle cell"
},
"taxa": "Homo sapiens"
},
{
"@id": "/in-vitro-systems/IGVFSM9326DRHX/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM9326DRHX",
"aliases": [
"nikhil-munshi:differentited_WTC11_CM_Pilot1_PB_LW238"
],
"classifications": [
"differentiated cell specimen"
],
"construct_library_sets": [
"/construct-library-sets/IGVFDS9629YZLO/"
],
"modifications": [
{
"@id": "/crispr-modifications/0a63b754-eca4-44aa-bbc2-fccdc6c44fb5/",
"modality": "interference",
"status": "preview"
}
],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0009747/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"aliases": [
"igvf:WTC11"
],
"status": "released",
"summary": "GM25256 (WTC-11)",
"term_name": "GM25256 (WTC-11)"
}
],
"status": "preview",
"summary": "GM25256 (WTC-11) differentiated cell specimen induced to cardiac muscle cell for 12 days (cellular sub pool: subpool_LW268), male, Homo sapiens modified with CRISPRi Sp-dCas9, transfected with a guide library",
"targeted_sample_term": {
"@id": "/sample-terms/CL_0000746/",
"status": "released",
"term_name": "cardiac muscle cell"
},
"taxa": "Homo sapiens"
},
{
"@id": "/in-vitro-systems/IGVFSM5652SBGF/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM5652SBGF",
"aliases": [
"nikhil-munshi:differentited_WTC11_CM_Pilot1_PB_LW236"
],
"classifications": [
"differentiated cell specimen"
],
"construct_library_sets": [
"/construct-library-sets/IGVFDS9629YZLO/"
],
"modifications": [
{
"@id": "/crispr-modifications/0a63b754-eca4-44aa-bbc2-fccdc6c44fb5/",
"modality": "interference",
"status": "preview"
}
],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0009747/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"aliases": [
"igvf:WTC11"
],
"status": "released",
"summary": "GM25256 (WTC-11)",
"term_name": "GM25256 (WTC-11)"
}
],
"status": "preview",
"summary": "GM25256 (WTC-11) differentiated cell specimen induced to cardiac muscle cell for 12 days (cellular sub pool: subpool_LW266), male, Homo sapiens modified with CRISPRi Sp-dCas9, transfected with a guide library",
"targeted_sample_term": {
"@id": "/sample-terms/CL_0000746/",
"status": "released",
"term_name": "cardiac muscle cell"
},
"taxa": "Homo sapiens"
},
{
"@id": "/in-vitro-systems/IGVFSM8137TZJW/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM8137TZJW",
"aliases": [
"nikhil-munshi:differentited_WTC11_CM_Pilot1_PB_LW234"
],
"classifications": [
"differentiated cell specimen"
],
"construct_library_sets": [
"/construct-library-sets/IGVFDS9629YZLO/"
],
"modifications": [
{
"@id": "/crispr-modifications/0a63b754-eca4-44aa-bbc2-fccdc6c44fb5/",
"modality": "interference",
"status": "preview"
}
],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0009747/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"aliases": [
"igvf:WTC11"
],
"status": "released",
"summary": "GM25256 (WTC-11)",
"term_name": "GM25256 (WTC-11)"
}
],
"status": "preview",
"summary": "GM25256 (WTC-11) differentiated cell specimen induced to cardiac muscle cell for 12 days (cellular sub pool: subpool_LW264), male, Homo sapiens modified with CRISPRi Sp-dCas9, transfected with a guide library",
"targeted_sample_term": {
"@id": "/sample-terms/CL_0000746/",
"status": "released",
"term_name": "cardiac muscle cell"
},
"taxa": "Homo sapiens"
},
{
"@id": "/in-vitro-systems/IGVFSM2930BIPX/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM2930BIPX",
"aliases": [
"nikhil-munshi:differentited_WTC11_CM_Pilot1_PB_LW235"
],
"classifications": [
"differentiated cell specimen"
],
"construct_library_sets": [
"/construct-library-sets/IGVFDS9629YZLO/"
],
"modifications": [
{
"@id": "/crispr-modifications/0a63b754-eca4-44aa-bbc2-fccdc6c44fb5/",
"modality": "interference",
"status": "preview"
}
],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0009747/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"aliases": [
"igvf:WTC11"
],
"status": "released",
"summary": "GM25256 (WTC-11)",
"term_name": "GM25256 (WTC-11)"
}
],
"status": "preview",
"summary": "GM25256 (WTC-11) differentiated cell specimen induced to cardiac muscle cell for 12 days (cellular sub pool: subpool_LW265), male, Homo sapiens modified with CRISPRi Sp-dCas9, transfected with a guide library",
"targeted_sample_term": {
"@id": "/sample-terms/CL_0000746/",
"status": "released",
"term_name": "cardiac muscle cell"
},
"taxa": "Homo sapiens"
},
{
"@id": "/in-vitro-systems/IGVFSM2329UXLZ/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM2329UXLZ",
"aliases": [
"nikhil-munshi:differentited_WTC11_CM_Pilot1_PB_LW237"
],
"classifications": [
"differentiated cell specimen"
],
"construct_library_sets": [
"/construct-library-sets/IGVFDS9629YZLO/"
],
"modifications": [
{
"@id": "/crispr-modifications/0a63b754-eca4-44aa-bbc2-fccdc6c44fb5/",
"modality": "interference",
"status": "preview"
}
],
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{
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