{
"@context": "/terms/",
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"@type": [
"AnalysisSet",
"FileSet",
"Item"
],
"accession": "IGVFDS6924DJAZ",
"aliases": [
"gary-hon:H9_CM_Pilot2_Mini_Inducible_PrimaryAnalysis"
],
"assay_titles": [
"Perturb-seq"
],
"audit": {
"ERROR": [
{
"category": "unexpected input file set",
"detail": "Analysis set [IGVFDS6924DJAZ](/analysis-sets/IGVFDS6924DJAZ/) links to file set(s): [IGVFDS3847PDAQ](/measurement-sets/IGVFDS3847PDAQ/), [IGVFDS4121IORO](/measurement-sets/IGVFDS4121IORO/), [IGVFDS8110KLML](/measurement-sets/IGVFDS8110KLML/), [IGVFDS9735REPA](/auxiliary-sets/IGVFDS9735REPA/), [IGVFDS0170TMBA](/auxiliary-sets/IGVFDS0170TMBA/), [IGVFDS6534GRPN](/auxiliary-sets/IGVFDS6534GRPN/), [IGVFDS1760WHSE](/auxiliary-sets/IGVFDS1760WHSE/), [IGVFDS0922ZREC](/measurement-sets/IGVFDS0922ZREC/), [IGVFDS7849GKLL](/auxiliary-sets/IGVFDS7849GKLL/), [IGVFDS3659SZDC](/auxiliary-sets/IGVFDS3659SZDC/), [IGVFDS8811SXIK](/auxiliary-sets/IGVFDS8811SXIK/), [IGVFDS6780UKAY](/auxiliary-sets/IGVFDS6780UKAY/) 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/IGVFDS6924DJAZ/"
},
{
"category": "upload status not validated",
"detail": "Tabular file [IGVFFI0068OWUG](/tabular-files/IGVFFI0068OWUG/) has `upload_status` invalidated. Validation error detail: {\"md5sum\": \"original md5sum 9f7307644d51e3727da0e1e26146df9f does not match newly calculated md5sum 50e87154d1777fce3921e0d3ee44e2d6.\"}. Files are expected to be validated or validation exempted.",
"level": 60,
"level_name": "ERROR",
"name": "audit_upload_status",
"path": "/tabular-files/IGVFFI0068OWUG/"
},
{
"category": "upload status not validated",
"detail": "Tabular file [IGVFFI7000QYPC](/tabular-files/IGVFFI7000QYPC/) has `upload_status` invalidated. Validation error detail: {\"md5sum\": \"original md5sum ba19258f0a94f724515239da49d125de does not match newly calculated md5sum 490d7528ec12b6ab7e3221730bcf71c4.\"}. Files are expected to be validated or validation exempted.",
"level": 60,
"level_name": "ERROR",
"name": "audit_upload_status",
"path": "/tabular-files/IGVFFI7000QYPC/"
}
],
"INTERNAL_ACTION": [
{
"category": "mismatched status",
"detail": "Preview matrix file [IGVFFI2138BRRC](/matrix-files/IGVFFI2138BRRC/) 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/IGVFFI2138BRRC/"
},
{
"category": "mismatched status",
"detail": "Preview matrix file [IGVFFI8522GXEK](/matrix-files/IGVFFI8522GXEK/) 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/IGVFFI8522GXEK/"
},
{
"category": "mismatched status",
"detail": "Preview matrix file [IGVFFI0015OJLL](/matrix-files/IGVFFI0015OJLL/) 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/IGVFFI0015OJLL/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing analysis step version",
"detail": "Analysis set [IGVFDS6924DJAZ](/analysis-sets/IGVFDS6924DJAZ/) links to file(s) [IGVFFI7000QYPC](/tabular-files/IGVFFI7000QYPC/), [IGVFFI0068OWUG](/tabular-files/IGVFFI0068OWUG/) 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/IGVFDS6924DJAZ/"
},
{
"category": "missing derived from",
"detail": "Analysis set [IGVFDS6924DJAZ](/analysis-sets/IGVFDS6924DJAZ/) links to file(s) [IGVFFI2138BRRC](/matrix-files/IGVFFI2138BRRC/), [IGVFFI8522GXEK](/matrix-files/IGVFFI8522GXEK/), [IGVFFI0015OJLL](/matrix-files/IGVFFI0015OJLL/), [IGVFFI7000QYPC](/tabular-files/IGVFFI7000QYPC/), [IGVFFI0068OWUG](/tabular-files/IGVFFI0068OWUG/) 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/IGVFDS6924DJAZ/"
},
{
"category": "missing file format specifications",
"detail": "Tabular file [IGVFFI0068OWUG](/tabular-files/IGVFFI0068OWUG/) 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/IGVFFI0068OWUG/"
},
{
"category": "missing file format specifications",
"detail": "Tabular file [IGVFFI7000QYPC](/tabular-files/IGVFFI7000QYPC/) 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/IGVFFI7000QYPC/"
}
]
},
"award": {
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"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": "2024-12-04T20:07:28.048770+00:00",
"donors": [
{
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"accession": "IGVFDO2718IDDQ",
"aliases": [
"igvf:donor_of_H9"
],
"sex": "female",
"status": "released",
"taxa": "Homo sapiens"
}
],
"file_set_type": "principal analysis",
"files": [
{
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"accession": "IGVFFI2138BRRC",
"aliases": [
"gary-hon:H9_CM_Pilot2_Mini_Inducible_PrimaryAnalysis_h5ad"
],
"content_type": "sparse gene count matrix",
"creation_timestamp": "2024-12-17T22:43:45.582362+00:00",
"file_format": "h5ad",
"file_size": 15538028955,
"href": "/matrix-files/IGVFFI2138BRRC/@@download/IGVFFI2138BRRC.h5ad",
"s3_uri": "s3://igvf-files/2024/12/17/c37784dd-7197-4617-9534-1c2900f8d49d/IGVFFI2138BRRC.h5ad",
"status": "preview",
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"upload_status": "validated"
},
{
"@id": "/matrix-files/IGVFFI8522GXEK/",
"accession": "IGVFFI8522GXEK",
"aliases": [
"gary-hon:H9_CM_Pilot2_Mini_Inducible_PrimaryAnalysis_h5"
],
"content_type": "filtered feature barcode matrix",
"creation_timestamp": "2024-12-17T23:41:57.834293+00:00",
"file_format": "hdf5",
"file_size": 512883457,
"href": "/matrix-files/IGVFFI8522GXEK/@@download/IGVFFI8522GXEK.h5",
"s3_uri": "s3://igvf-files/2024/12/17/c108eba2-7571-464d-a98d-ea4b84fb2c34/IGVFFI8522GXEK.h5",
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/s215194/Single_Cell/mini_cm_pilot_02_inducible/_421-424_inducible/_aggr_transcriptome/cm_pilot_mini_02_no_normalization_inducible/outs/count/filtered_feature_bc_matrix.h5",
"upload_status": "validated"
},
{
"@id": "/matrix-files/IGVFFI0015OJLL/",
"accession": "IGVFFI0015OJLL",
"aliases": [
"gary-hon:H9_CM_Pilot2_Mini_Inducible_PrimaryAnalysis_pkl"
],
"content_type": "raw feature barcode matrix",
"creation_timestamp": "2024-12-17T23:42:11.932982+00:00",
"file_format": "pkl",
"file_size": 1898796914,
"href": "/matrix-files/IGVFFI0015OJLL/@@download/IGVFFI0015OJLLpkl",
"s3_uri": "s3://igvf-files/2024/12/17/f5dabb69-5609-4b4f-9ebc-aae6bc1a852e/IGVFFI0015OJLLpkl",
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/s215194/Single_Cell/mini_cm_pilot_02_inducible/_421-424_inducible/aggr_dataframe/aggr_combined_df_full.pkl",
"upload_status": "validated"
},
{
"@id": "/tabular-files/IGVFFI7000QYPC/",
"accession": "IGVFFI7000QYPC",
"aliases": [
"gary-hon:H9_CM_Pilot2_Mini_Inducible_PrimaryAnalysis_DE_local"
],
"content_type": "unfiltered local differential expression",
"controlled_access": false,
"creation_timestamp": "2024-12-18T20:47:10.852788+00:00",
"file_format": "csv",
"file_size": 5184,
"href": "/tabular-files/IGVFFI7000QYPC/@@download/IGVFFI7000QYPC.csv.gz",
"s3_uri": "s3://igvf-files/2024/12/18/5c457fdf-898c-4e58-8e8e-3ba4307880fc/IGVFFI7000QYPC.csv.gz",
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/s215194/IGVF/data_submission/reference_files/H9_CM_Pilot2_Mini_Inducible_PrimaryAnalysis_DE_local.csv.gz",
"upload_status": "invalidated"
},
{
"@id": "/tabular-files/IGVFFI0068OWUG/",
"accession": "IGVFFI0068OWUG",
"aliases": [
"gary-hon:H9_CM_Pilot2_Mini_Inducible_PrimaryAnalysis_DE_global"
],
"content_type": "unfiltered global differential expression",
"controlled_access": false,
"creation_timestamp": "2024-12-18T20:47:25.661952+00:00",
"file_format": "csv",
"file_size": 132567,
"href": "/tabular-files/IGVFFI0068OWUG/@@download/IGVFFI0068OWUG.csv.gz",
"s3_uri": "s3://igvf-files/2024/12/18/8026677e-fd90-47d2-b344-9f6076df0a7b/IGVFFI0068OWUG.csv.gz",
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/s215194/IGVF/data_submission/reference_files/H9_CM_Pilot2_Mini_Inducible_PrimaryAnalysis_DE_global.csv.gz",
"upload_status": "invalidated"
}
],
"functional_assay_mechanisms": [],
"input_file_sets": [
{
"@id": "/measurement-sets/IGVFDS0922ZREC/",
"accession": "IGVFDS0922ZREC",
"aliases": [
"gary-hon:differentited_H9_CM_Pilot2_Mini_Inducible_LW421"
],
"file_set_type": "experimental data",
"status": "preview"
},
{
"@id": "/auxiliary-sets/IGVFDS6534GRPN/",
"accession": "IGVFDS6534GRPN",
"aliases": [
"gary-hon:differentited_H9_CM_Pilot2_Mini_Inducible_sgRNA_LW421"
],
"file_set_type": "gRNA sequencing",
"status": "preview"
},
{
"@id": "/auxiliary-sets/IGVFDS6780UKAY/",
"accession": "IGVFDS6780UKAY",
"aliases": [
"gary-hon:differentited_H9_CM_Pilot2_Mini_Inducible_HTO_LW421"
],
"file_set_type": "cell hashing barcode sequencing",
"status": "preview"
},
{
"@id": "/measurement-sets/IGVFDS4121IORO/",
"accession": "IGVFDS4121IORO",
"aliases": [
"gary-hon:differentited_H9_CM_Pilot2_Mini_Inducible_LW422"
],
"file_set_type": "experimental data",
"status": "preview"
},
{
"@id": "/auxiliary-sets/IGVFDS0170TMBA/",
"accession": "IGVFDS0170TMBA",
"aliases": [
"gary-hon:differentited_H9_CM_Pilot2_Mini_Inducible_sgRNA_LW422"
],
"file_set_type": "gRNA sequencing",
"status": "preview"
},
{
"@id": "/auxiliary-sets/IGVFDS1760WHSE/",
"accession": "IGVFDS1760WHSE",
"aliases": [
"gary-hon:differentited_H9_CM_Pilot2_Mini_Inducible_HTO_LW422"
],
"file_set_type": "cell hashing barcode sequencing",
"status": "preview"
},
{
"@id": "/measurement-sets/IGVFDS3847PDAQ/",
"accession": "IGVFDS3847PDAQ",
"aliases": [
"gary-hon:differentited_H9_CM_Pilot2_Mini_Inducible_LW423"
],
"file_set_type": "experimental data",
"status": "preview"
},
{
"@id": "/auxiliary-sets/IGVFDS9735REPA/",
"accession": "IGVFDS9735REPA",
"aliases": [
"gary-hon:differentited_H9_CM_Pilot2_Mini_Inducible_sgRNA_LW423"
],
"file_set_type": "gRNA sequencing",
"status": "preview"
},
{
"@id": "/auxiliary-sets/IGVFDS8811SXIK/",
"accession": "IGVFDS8811SXIK",
"aliases": [
"gary-hon:differentited_H9_CM_Pilot2_Mini_Inducible_HTO_LW423"
],
"file_set_type": "cell hashing barcode sequencing",
"status": "preview"
},
{
"@id": "/measurement-sets/IGVFDS8110KLML/",
"accession": "IGVFDS8110KLML",
"aliases": [
"gary-hon:differentited_H9_CM_Pilot2_Mini_Inducible_LW424"
],
"file_set_type": "experimental data",
"status": "preview"
},
{
"@id": "/auxiliary-sets/IGVFDS3659SZDC/",
"accession": "IGVFDS3659SZDC",
"aliases": [
"gary-hon:differentited_H9_CM_Pilot2_Mini_Inducible_sgRNA_LW424"
],
"file_set_type": "gRNA sequencing",
"status": "preview"
},
{
"@id": "/auxiliary-sets/IGVFDS7849GKLL/",
"accession": "IGVFDS7849GKLL",
"aliases": [
"gary-hon:differentited_H9_CM_Pilot2_Mini_Inducible_HTO_LW424"
],
"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/IGVFSM3002CFHI/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM3002CFHI",
"aliases": [
"nikhil-munshi:differentited_H9_CM_Pilot2_Mini_Inducible_LW424"
],
"classifications": [
"differentiated cell specimen"
],
"construct_library_sets": [
"/construct-library-sets/IGVFDS0346MQBH/"
],
"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_LW424), 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/IGVFSM8986CPUS/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM8986CPUS",
"aliases": [
"nikhil-munshi:differentited_H9_CM_Pilot2_Mini_Inducible_LW422"
],
"classifications": [
"differentiated cell specimen"
],
"construct_library_sets": [
"/construct-library-sets/IGVFDS0346MQBH/"
],
"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_LW422), 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/IGVFSM3015ZQZL/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM3015ZQZL",
"aliases": [
"nikhil-munshi:differentited_H9_CM_Pilot2_Mini_Inducible_LW423"
],
"classifications": [
"differentiated cell specimen"
],
"construct_library_sets": [
"/construct-library-sets/IGVFDS0346MQBH/"
],
"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_LW423), 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/IGVFSM3680SAKS/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM3680SAKS",
"aliases": [
"nikhil-munshi:differentited_H9_CM_Pilot2_Mini_Inducible_LW421"
],
"classifications": [
"differentiated cell specimen"
],
"construct_library_sets": [
"/construct-library-sets/IGVFDS0346MQBH/"
],
"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_LW421), 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": "2024-12-17T22:43:45.582362+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": "fb99666b-1d9e-4b74-b8ec-d87f0775372c",
"workflows": [
{
"@id": "/workflows/IGVFWF0190YALU/",
"accession": "IGVFWF0190YALU",
"name": "Hon Perturb-seq Workflow",
"status": "in progress",
"uniform_pipeline": false
}
]
}