{
"@context": "/terms/",
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"AnalysisSet",
"FileSet",
"Item"
],
"accession": "IGVFDS2873EPIU",
"aliases": [
"gary-hon:H9_shen_construct_sgRNA_Lenti_PrimaryAnalysis"
],
"assay_titles": [
"Perturb-seq"
],
"audit": {
"ERROR": [
{
"category": "upload status not validated",
"detail": "Tabular file [IGVFFI0726ZROO](/tabular-files/IGVFFI0726ZROO/) has `upload_status` invalidated. Validation error detail: {\"md5sum\": \"original md5sum db6bfdd27563f942b448b19a54c81ca2 does not match newly calculated md5sum aacd3987ffef6d086350c35bd117af1d.\"}. Files are expected to be validated or validation exempted.",
"level": 60,
"level_name": "ERROR",
"name": "audit_upload_status",
"path": "/tabular-files/IGVFFI0726ZROO/"
},
{
"category": "unexpected input file set",
"detail": "Analysis set [IGVFDS2873EPIU](/analysis-sets/IGVFDS2873EPIU/) links to file set(s): [IGVFDS8999BYPM](/auxiliary-sets/IGVFDS8999BYPM/), [IGVFDS6931FVDN](/auxiliary-sets/IGVFDS6931FVDN/), [IGVFDS2962WEZD](/auxiliary-sets/IGVFDS2962WEZD/), [IGVFDS2739QDQI](/auxiliary-sets/IGVFDS2739QDQI/), [IGVFDS4940ELQK](/measurement-sets/IGVFDS4940ELQK/), [IGVFDS5158EDZB](/measurement-sets/IGVFDS5158EDZB/), [IGVFDS3876QHZN](/measurement-sets/IGVFDS3876QHZN/), [IGVFDS8839RSIR](/auxiliary-sets/IGVFDS8839RSIR/), [IGVFDS1004SBHR](/auxiliary-sets/IGVFDS1004SBHR/), [IGVFDS5720GLEJ](/auxiliary-sets/IGVFDS5720GLEJ/), [IGVFDS8726ORVQ](/auxiliary-sets/IGVFDS8726ORVQ/), [IGVFDS8449CDOE](/measurement-sets/IGVFDS8449CDOE/) 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/IGVFDS2873EPIU/"
},
{
"category": "upload status not validated",
"detail": "Tabular file [IGVFFI8243SXOZ](/tabular-files/IGVFFI8243SXOZ/) has `upload_status` invalidated. Validation error detail: {\"md5sum\": \"original md5sum f7c65e9de4928af51728a463aa43f4ee does not match newly calculated md5sum 3e96c1b9a391716f846b7aa189e72e39.\"}. Files are expected to be validated or validation exempted.",
"level": 60,
"level_name": "ERROR",
"name": "audit_upload_status",
"path": "/tabular-files/IGVFFI8243SXOZ/"
}
],
"INTERNAL_ACTION": [
{
"category": "mismatched status",
"detail": "Preview matrix file [IGVFFI9418VTSZ](/matrix-files/IGVFFI9418VTSZ/) 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/IGVFFI9418VTSZ/"
},
{
"category": "mismatched status",
"detail": "Preview matrix file [IGVFFI4183MEQT](/matrix-files/IGVFFI4183MEQT/) 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/IGVFFI4183MEQT/"
},
{
"category": "mismatched status",
"detail": "Preview matrix file [IGVFFI3849WCSB](/matrix-files/IGVFFI3849WCSB/) 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/IGVFFI3849WCSB/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing file format specifications",
"detail": "Tabular file [IGVFFI0726ZROO](/tabular-files/IGVFFI0726ZROO/) has no `file_format_specifications`. Tabular files are expected to link to a file format specifications document describing the headers of the file.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_tabular_file_no_file_format_specifications",
"path": "/tabular-files/IGVFFI0726ZROO/"
},
{
"category": "missing analysis step version",
"detail": "Analysis set [IGVFDS2873EPIU](/analysis-sets/IGVFDS2873EPIU/) links to file(s) [IGVFFI8243SXOZ](/tabular-files/IGVFFI8243SXOZ/), [IGVFFI0726ZROO](/tabular-files/IGVFFI0726ZROO/) that are missing `analysis_step_version`. Analysis set files are expected to specify analysis step version.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_analysis_set_files_missing_analysis_step_version",
"path": "/analysis-sets/IGVFDS2873EPIU/"
},
{
"category": "missing derived from",
"detail": "Analysis set [IGVFDS2873EPIU](/analysis-sets/IGVFDS2873EPIU/) links to file(s) [IGVFFI9418VTSZ](/matrix-files/IGVFFI9418VTSZ/), [IGVFFI3849WCSB](/matrix-files/IGVFFI3849WCSB/), [IGVFFI4183MEQT](/matrix-files/IGVFFI4183MEQT/), [IGVFFI8243SXOZ](/tabular-files/IGVFFI8243SXOZ/), [IGVFFI0726ZROO](/tabular-files/IGVFFI0726ZROO/) 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/IGVFDS2873EPIU/"
},
{
"category": "missing file format specifications",
"detail": "Tabular file [IGVFFI8243SXOZ](/tabular-files/IGVFFI8243SXOZ/) has no `file_format_specifications`. Tabular files are expected to link to a file format specifications document describing the headers of the file.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_tabular_file_no_file_format_specifications",
"path": "/tabular-files/IGVFFI8243SXOZ/"
}
]
},
"award": {
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"contact_pi": {
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"title": "Gary Hon"
},
"title": "Multiscale functional characterization of genomic variation in human developmental disorders"
},
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"donors": [
{
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"aliases": [
"igvf:donor_of_H9"
],
"sex": "female",
"status": "released",
"taxa": "Homo sapiens"
}
],
"file_set_type": "principal analysis",
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{
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"aliases": [
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],
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"creation_timestamp": "2024-12-17T22:40:22.860427+00:00",
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"upload_status": "validated"
},
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"aliases": [
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],
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"creation_timestamp": "2024-12-17T23:40:56.627478+00:00",
"file_format": "hdf5",
"file_size": 426149563,
"href": "/matrix-files/IGVFFI3849WCSB/@@download/IGVFFI3849WCSB.h5",
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"upload_status": "validated"
},
{
"@id": "/matrix-files/IGVFFI4183MEQT/",
"accession": "IGVFFI4183MEQT",
"aliases": [
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],
"content_type": "raw feature barcode matrix",
"creation_timestamp": "2024-12-17T23:41:10.318077+00:00",
"file_format": "pkl",
"file_size": 1366432004,
"href": "/matrix-files/IGVFFI4183MEQT/@@download/IGVFFI4183MEQTpkl",
"s3_uri": "s3://igvf-files/2024/12/17/6c7163d3-6da5-44be-abf5-f8c1e200d997/IGVFFI4183MEQTpkl",
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"upload_status": "validated"
},
{
"@id": "/tabular-files/IGVFFI8243SXOZ/",
"accession": "IGVFFI8243SXOZ",
"aliases": [
"gary-hon:H9_shen_construct_sgRNA_Lenti_PrimaryAnalysis_DE_local"
],
"content_type": "unfiltered local differential expression",
"controlled_access": false,
"creation_timestamp": "2024-12-18T19:31:25.771546+00:00",
"file_format": "csv",
"file_size": 4106,
"href": "/tabular-files/IGVFFI8243SXOZ/@@download/IGVFFI8243SXOZ.csv.gz",
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"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/s215194/IGVF/data_submission/reference_files/H9_shen_construct_sgRNA_Lenti_PrimaryAnalysis_DE_local.csv.gz",
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},
{
"@id": "/tabular-files/IGVFFI0726ZROO/",
"accession": "IGVFFI0726ZROO",
"aliases": [
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],
"content_type": "unfiltered global differential expression",
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"creation_timestamp": "2024-12-19T15:49:05.729607+00:00",
"file_format": "csv",
"file_size": 285499,
"href": "/tabular-files/IGVFFI0726ZROO/@@download/IGVFFI0726ZROO.csv.gz",
"s3_uri": "s3://igvf-files/2024/12/19/8009d0fe-97be-4993-bceb-e46b2368145e/IGVFFI0726ZROO.csv.gz",
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/s215194/IGVF/data_submission/reference_files/H9_shen_construct_sgRNA_Lenti_PrimaryAnalysis_DE_global.csv.gz",
"upload_status": "invalidated"
}
],
"functional_assay_mechanisms": [],
"input_file_sets": [
{
"@id": "/measurement-sets/IGVFDS3876QHZN/",
"accession": "IGVFDS3876QHZN",
"aliases": [
"gary-hon:CM_Pilot_2_Mini_Lenti_LW269"
],
"file_set_type": "experimental data",
"status": "preview"
},
{
"@id": "/auxiliary-sets/IGVFDS2962WEZD/",
"accession": "IGVFDS2962WEZD",
"aliases": [
"gary-hon:CM_Pilot_2_Mini_sgRNA_Lenti_LW269"
],
"file_set_type": "gRNA sequencing",
"status": "preview"
},
{
"@id": "/auxiliary-sets/IGVFDS5720GLEJ/",
"accession": "IGVFDS5720GLEJ",
"aliases": [
"gary-hon:CM_Pilot_2_Mini_HTO_Lenti_LW269"
],
"file_set_type": "cell hashing barcode sequencing",
"status": "preview"
},
{
"@id": "/measurement-sets/IGVFDS5158EDZB/",
"accession": "IGVFDS5158EDZB",
"aliases": [
"gary-hon:CM_Pilot_2_Mini_Lenti_LW270"
],
"file_set_type": "experimental data",
"status": "preview"
},
{
"@id": "/auxiliary-sets/IGVFDS6931FVDN/",
"accession": "IGVFDS6931FVDN",
"aliases": [
"gary-hon:CM_Pilot_2_Mini_sgRNA_Lenti_LW270"
],
"file_set_type": "gRNA sequencing",
"status": "preview"
},
{
"@id": "/auxiliary-sets/IGVFDS8999BYPM/",
"accession": "IGVFDS8999BYPM",
"aliases": [
"gary-hon:CM_Pilot_2_Mini_HTO_Lenti_LW270"
],
"file_set_type": "cell hashing barcode sequencing",
"status": "preview"
},
{
"@id": "/measurement-sets/IGVFDS8449CDOE/",
"accession": "IGVFDS8449CDOE",
"aliases": [
"gary-hon:CM_Pilot_2_Mini_Lenti_LW271"
],
"file_set_type": "experimental data",
"status": "preview"
},
{
"@id": "/auxiliary-sets/IGVFDS1004SBHR/",
"accession": "IGVFDS1004SBHR",
"aliases": [
"gary-hon:CM_Pilot_2_Mini_sgRNA_Lenti_LW271"
],
"file_set_type": "gRNA sequencing",
"status": "preview"
},
{
"@id": "/auxiliary-sets/IGVFDS2739QDQI/",
"accession": "IGVFDS2739QDQI",
"aliases": [
"gary-hon:CM_Pilot_2_Mini_HTO_Lenti_LW271"
],
"file_set_type": "cell hashing barcode sequencing",
"status": "preview"
},
{
"@id": "/measurement-sets/IGVFDS4940ELQK/",
"accession": "IGVFDS4940ELQK",
"aliases": [
"gary-hon:CM_Pilot_2_Mini_Lenti_LW272"
],
"file_set_type": "experimental data",
"status": "preview"
},
{
"@id": "/auxiliary-sets/IGVFDS8726ORVQ/",
"accession": "IGVFDS8726ORVQ",
"aliases": [
"gary-hon:CM_Pilot_2_Mini_sgRNA_Lenti_LW272"
],
"file_set_type": "gRNA sequencing",
"status": "preview"
},
{
"@id": "/auxiliary-sets/IGVFDS8839RSIR/",
"accession": "IGVFDS8839RSIR",
"aliases": [
"gary-hon:CM_Pilot_2_Mini_HTO_Lenti_LW272"
],
"file_set_type": "cell hashing barcode sequencing",
"status": "preview"
}
],
"input_for": [],
"lab": {
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"title": "Gary Hon, UT"
},
"protocols": [
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],
"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/IGVFSM9223FAYO/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM9223FAYO",
"aliases": [
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],
"classifications": [
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],
"construct_library_sets": [
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],
"modifications": [
{
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"modality": "interference",
"status": "preview"
}
],
"sample_terms": [
{
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"@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_LW269), female, Homo sapiens modified with CRISPRi Sp-dCas9, transduced (lentivirus) with a guide library",
"targeted_sample_term": {
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"status": "released",
"term_name": "cardiac muscle cell"
},
"taxa": "Homo sapiens"
},
{
"@id": "/in-vitro-systems/IGVFSM1608DJBB/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM1608DJBB",
"aliases": [
"gary-hon:differentiated_H9_shen_construct_sgRNA_Lenti_LW272"
],
"classifications": [
"differentiated cell specimen"
],
"construct_library_sets": [
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],
"modifications": [
{
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"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_LW272), female, Homo sapiens modified with CRISPRi Sp-dCas9, transduced (lentivirus) 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/IGVFSM5657YKPN/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM5657YKPN",
"aliases": [
"gary-hon:differentiated_H9_shen_construct_sgRNA_Lenti_LW271"
],
"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_LW271), female, Homo sapiens modified with CRISPRi Sp-dCas9, transduced (lentivirus) 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/IGVFSM6628JOOL/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM6628JOOL",
"aliases": [
"gary-hon:differentiated_H9_shen_construct_sgRNA_Lenti_LW270"
],
"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_LW270), female, Homo sapiens modified with CRISPRi Sp-dCas9, transduced (lentivirus) 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": "2024-12-17T22:40:22.860427+00:00",
"summary": "interference Perturb-seq: filtered feature barcode matrix, raw feature barcode matrix, sparse gene count matrix, unfiltered global differential expression, unfiltered local differential expression",
"uuid": "6e80e187-6bc9-4ce0-b56e-c690651a5cc4",
"workflows": [
{
"@id": "/workflows/IGVFWF0190YALU/",
"accession": "IGVFWF0190YALU",
"name": "Hon Perturb-seq Workflow",
"status": "in progress",
"uniform_pipeline": false
}
]
}