{
"@context": "/terms/",
"@id": "/analysis-sets/IGVFDS4762GRIW/",
"@type": [
"AnalysisSet",
"FileSet",
"Item"
],
"accession": "IGVFDS4762GRIW",
"aliases": [
"gary-hon:H9_shen_construct_sgRNA_PB_PrimaryAnalysis"
],
"assay_titles": [
"Perturb-seq"
],
"audit": {
"ERROR": [
{
"category": "unexpected input file set",
"detail": "Analysis set [IGVFDS4762GRIW](/analysis-sets/IGVFDS4762GRIW/) links to file set(s): [IGVFDS5643OMJV](/auxiliary-sets/IGVFDS5643OMJV/), [IGVFDS7977FNRB](/auxiliary-sets/IGVFDS7977FNRB/), [IGVFDS1050IJPU](/measurement-sets/IGVFDS1050IJPU/), [IGVFDS0235TTEW](/measurement-sets/IGVFDS0235TTEW/), [IGVFDS4359ZBDC](/auxiliary-sets/IGVFDS4359ZBDC/), [IGVFDS5841QQSW](/auxiliary-sets/IGVFDS5841QQSW/), [IGVFDS4510VNEU](/auxiliary-sets/IGVFDS4510VNEU/), [IGVFDS2083PYXJ](/measurement-sets/IGVFDS2083PYXJ/), [IGVFDS9721PIUS](/auxiliary-sets/IGVFDS9721PIUS/), [IGVFDS6756DREO](/auxiliary-sets/IGVFDS6756DREO/), [IGVFDS0307GWPA](/measurement-sets/IGVFDS0307GWPA/), [IGVFDS5514EBWS](/auxiliary-sets/IGVFDS5514EBWS/) 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/IGVFDS4762GRIW/"
}
],
"INTERNAL_ACTION": [
{
"category": "mismatched status",
"detail": "Preview matrix file [IGVFFI9229XCVW](/matrix-files/IGVFFI9229XCVW/) 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/IGVFFI9229XCVW/"
},
{
"category": "mismatched status",
"detail": "Preview matrix file [IGVFFI0670VYBH](/matrix-files/IGVFFI0670VYBH/) 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/IGVFFI0670VYBH/"
},
{
"category": "mismatched status",
"detail": "Preview matrix file [IGVFFI2745PVKV](/matrix-files/IGVFFI2745PVKV/) 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/IGVFFI2745PVKV/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing derived from",
"detail": "Analysis set [IGVFDS4762GRIW](/analysis-sets/IGVFDS4762GRIW/) links to file(s) [IGVFFI0670VYBH](/matrix-files/IGVFFI0670VYBH/), [IGVFFI2745PVKV](/matrix-files/IGVFFI2745PVKV/), [IGVFFI9229XCVW](/matrix-files/IGVFFI9229XCVW/) 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/IGVFDS4762GRIW/"
}
]
},
"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": "2024-12-04T20:07:23.893529+00:00",
"donors": [
{
"@id": "/human-donors/IGVFDO2718IDDQ/",
"accession": "IGVFDO2718IDDQ",
"aliases": [
"igvf:donor_of_H9"
],
"sex": "female",
"status": "released",
"taxa": "Homo sapiens"
}
],
"file_set_type": "principal analysis",
"files": [
{
"@id": "/matrix-files/IGVFFI0670VYBH/",
"accession": "IGVFFI0670VYBH",
"aliases": [
"gary-hon:H9_shen_construct_sgRNA_PB_PrimaryAnalysis_h5ad"
],
"content_type": "sparse gene count matrix",
"creation_timestamp": "2024-12-17T22:42:18.099309+00:00",
"file_format": "h5ad",
"file_size": 8410152219,
"href": "/matrix-files/IGVFFI0670VYBH/@@download/IGVFFI0670VYBH.h5ad",
"s3_uri": "s3://igvf-files/2024/12/17/857368ea-76a3-4358-9613-c2a8a709cf0e/IGVFFI0670VYBH.h5ad",
"status": "preview",
"submitted_file_name": "/project/shared/gcrb_igvf/data/shared/CMPILOT2_Mini_PB_scRNAseq/H5AD/V0_cmpilot2_mini_sgRNACells_PB.h5ad",
"upload_status": "validated"
},
{
"@id": "/matrix-files/IGVFFI2745PVKV/",
"accession": "IGVFFI2745PVKV",
"aliases": [
"gary-hon:H9_shen_construct_sgRNA_PB_PrimaryAnalysis_h5"
],
"content_type": "filtered feature barcode matrix",
"creation_timestamp": "2024-12-17T23:41:31.035017+00:00",
"file_format": "hdf5",
"file_size": 425309477,
"href": "/matrix-files/IGVFFI2745PVKV/@@download/IGVFFI2745PVKV.h5",
"s3_uri": "s3://igvf-files/2024/12/17/14d1b441-2c85-4d7a-a097-67bbfb7870f0/IGVFFI2745PVKV.h5",
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/s215194/Single_Cell/Process_scRNA_CMPILOT2_Mini_/cm_pilot2_mini_pb/outs/count/filtered_feature_bc_matrix.h5",
"upload_status": "validated"
},
{
"@id": "/matrix-files/IGVFFI9229XCVW/",
"accession": "IGVFFI9229XCVW",
"aliases": [
"gary-hon:H9_shen_construct_sgRNA_PB_PrimaryAnalysis_pkl"
],
"content_type": "raw feature barcode matrix",
"creation_timestamp": "2024-12-17T23:41:42.749794+00:00",
"file_format": "pkl",
"file_size": 788786476,
"href": "/matrix-files/IGVFFI9229XCVW/@@download/IGVFFI9229XCVWpkl",
"s3_uri": "s3://igvf-files/2024/12/17/7c41999e-e079-45f0-87c4-756ccd42629d/IGVFFI9229XCVWpkl",
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/s215194/Single_Cell/Process_scRNA_CMPILOT2_Mini_/AGGR_CombinedFilt_Singlets_sgRNA_DF_NaN_adjusted_PB_2.pkl",
"upload_status": "validated"
}
],
"functional_assay_mechanisms": [],
"input_file_sets": [
{
"@id": "/measurement-sets/IGVFDS1050IJPU/",
"accession": "IGVFDS1050IJPU",
"aliases": [
"gary-hon:CM_Pilot_2_Mini_PB_LW273"
],
"file_set_type": "experimental data",
"status": "preview"
},
{
"@id": "/auxiliary-sets/IGVFDS5841QQSW/",
"accession": "IGVFDS5841QQSW",
"aliases": [
"gary-hon:CM_Pilot_2_Mini_sgRNA_PB_LW273"
],
"file_set_type": "gRNA sequencing",
"status": "preview"
},
{
"@id": "/auxiliary-sets/IGVFDS7977FNRB/",
"accession": "IGVFDS7977FNRB",
"aliases": [
"gary-hon:CM_Pilot_2_Mini_HTO_PB_LW273"
],
"file_set_type": "cell hashing barcode sequencing",
"status": "preview"
},
{
"@id": "/measurement-sets/IGVFDS0235TTEW/",
"accession": "IGVFDS0235TTEW",
"aliases": [
"gary-hon:CM_Pilot_2_Mini_PB_LW274"
],
"file_set_type": "experimental data",
"status": "preview"
},
{
"@id": "/auxiliary-sets/IGVFDS5514EBWS/",
"accession": "IGVFDS5514EBWS",
"aliases": [
"gary-hon:CM_Pilot_2_Mini_sgRNA_PB_LW274"
],
"file_set_type": "gRNA sequencing",
"status": "preview"
},
{
"@id": "/auxiliary-sets/IGVFDS5643OMJV/",
"accession": "IGVFDS5643OMJV",
"aliases": [
"gary-hon:CM_Pilot_2_Mini_HTO_PB_LW274"
],
"file_set_type": "cell hashing barcode sequencing",
"status": "preview"
},
{
"@id": "/measurement-sets/IGVFDS2083PYXJ/",
"accession": "IGVFDS2083PYXJ",
"aliases": [
"gary-hon:CM_Pilot_2_Mini_PB_LW275"
],
"file_set_type": "experimental data",
"status": "preview"
},
{
"@id": "/auxiliary-sets/IGVFDS9721PIUS/",
"accession": "IGVFDS9721PIUS",
"aliases": [
"gary-hon:CM_Pilot_2_Mini_sgRNA_PB_LW275"
],
"file_set_type": "gRNA sequencing",
"status": "preview"
},
{
"@id": "/auxiliary-sets/IGVFDS4359ZBDC/",
"accession": "IGVFDS4359ZBDC",
"aliases": [
"gary-hon:CM_Pilot_2_Mini_HTO_PB_LW275"
],
"file_set_type": "cell hashing barcode sequencing",
"status": "preview"
},
{
"@id": "/measurement-sets/IGVFDS0307GWPA/",
"accession": "IGVFDS0307GWPA",
"aliases": [
"gary-hon:CM_Pilot_2_Mini_PB_LW276"
],
"file_set_type": "experimental data",
"status": "preview"
},
{
"@id": "/auxiliary-sets/IGVFDS4510VNEU/",
"accession": "IGVFDS4510VNEU",
"aliases": [
"gary-hon:CM_Pilot_2_Mini_sgRNA_PB_LW276"
],
"file_set_type": "gRNA sequencing",
"status": "preview"
},
{
"@id": "/auxiliary-sets/IGVFDS6756DREO/",
"accession": "IGVFDS6756DREO",
"aliases": [
"gary-hon:CM_Pilot_2_Mini_HTO_PB_LW276"
],
"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": "H9 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/IGVFSM9532RAXS/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM9532RAXS",
"aliases": [
"gary-hon:differentiated_H9_shen_construct_sgRNA_PB_LW275"
],
"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_0003045/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"aliases": [
"igvf:H9"
],
"status": "released",
"summary": "H9",
"term_name": "H9"
}
],
"status": "preview",
"summary": "H9 differentiated cell specimen induced to cardiac muscle cell for 12 days (cellular sub pool: subpool_LW275), female, 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/IGVFSM1063UQVF/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM1063UQVF",
"aliases": [
"gary-hon:differentiated_H9_shen_construct_sgRNA_PB_LW273"
],
"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_0003045/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"aliases": [
"igvf:H9"
],
"status": "released",
"summary": "H9",
"term_name": "H9"
}
],
"status": "preview",
"summary": "H9 differentiated cell specimen induced to cardiac muscle cell for 12 days (cellular sub pool: subpool_LW273), female, 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/IGVFSM5849QIEI/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM5849QIEI",
"aliases": [
"gary-hon:differentiated_H9_shen_construct_sgRNA_PB_LW274"
],
"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_0003045/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"aliases": [
"igvf:H9"
],
"status": "released",
"summary": "H9",
"term_name": "H9"
}
],
"status": "preview",
"summary": "H9 differentiated cell specimen induced to cardiac muscle cell for 12 days (cellular sub pool: subpool_LW274), female, 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/IGVFSM6716LOHW/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM6716LOHW",
"aliases": [
"gary-hon:differentiated_H9_shen_construct_sgRNA_PB_LW276"
],
"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_0003045/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"aliases": [
"igvf:H9"
],
"status": "released",
"summary": "H9",
"term_name": "H9"
}
],
"status": "preview",
"summary": "H9 differentiated cell specimen induced to cardiac muscle cell for 12 days (cellular sub pool: subpool_LW276), female, 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"
}
],
"schema_version": "9",
"status": "preview",
"submitted_by": {
"@id": "/users/b05645f1-2d56-4a5e-b272-4601e555a3fa/",
"title": "Mpathi Nzima"
},
"submitted_files_timestamp": "2024-12-17T22:42:18.099309+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": "1ed723b0-b5d0-46f9-8f93-78ee61b0c227",
"workflows": [
{
"@id": "/workflows/IGVFWF0190YALU/",
"accession": "IGVFWF0190YALU",
"name": "Hon Perturb-seq Workflow",
"status": "in progress",
"uniform_pipeline": false
}
]
}