{
"@context": "/terms/",
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"@type": [
"AnalysisSet",
"FileSet",
"Item"
],
"accession": "IGVFDS4252LFRU",
"aliases": [
"gary-hon:WTC11_CM_Pilot2_Mini_PB9_PrimaryAnalysis"
],
"assay_titles": [
"Perturb-seq"
],
"audit": {
"ERROR": [
{
"category": "upload status not validated",
"detail": "Tabular file [IGVFFI4410YZQZ](/tabular-files/IGVFFI4410YZQZ/) has `upload_status` invalidated. Validation error detail: {\"md5sum\": \"original md5sum 521928c40e2bdf2234d01082cf035998 does not match newly calculated md5sum 5529ced80d67d34b604a49a2e7a0404a.\"}. Files are expected to be validated or validation exempted.",
"level": 60,
"level_name": "ERROR",
"name": "audit_upload_status",
"path": "/tabular-files/IGVFFI4410YZQZ/"
},
{
"category": "upload status not validated",
"detail": "Tabular file [IGVFFI8786YBUA](/tabular-files/IGVFFI8786YBUA/) has `upload_status` invalidated. Validation error detail: {\"md5sum\": \"original md5sum 8475fc7d510636e9ce69059573955f41 does not match newly calculated md5sum a6f6f1723cf01626f1f1df693dc3208f.\"}. Files are expected to be validated or validation exempted.",
"level": 60,
"level_name": "ERROR",
"name": "audit_upload_status",
"path": "/tabular-files/IGVFFI8786YBUA/"
},
{
"category": "unexpected input file set",
"detail": "Analysis set [IGVFDS4252LFRU](/analysis-sets/IGVFDS4252LFRU/) links to file set(s): [IGVFDS8878JVPZ](/auxiliary-sets/IGVFDS8878JVPZ/), [IGVFDS3881UZJT](/auxiliary-sets/IGVFDS3881UZJT/), [IGVFDS5210TKRS](/auxiliary-sets/IGVFDS5210TKRS/), [IGVFDS9289FWZN](/auxiliary-sets/IGVFDS9289FWZN/), [IGVFDS9781HZZV](/auxiliary-sets/IGVFDS9781HZZV/), [IGVFDS7818HFMO](/measurement-sets/IGVFDS7818HFMO/), [IGVFDS0373CFJS](/auxiliary-sets/IGVFDS0373CFJS/), [IGVFDS3701EFIG](/auxiliary-sets/IGVFDS3701EFIG/), [IGVFDS1417TPKZ](/auxiliary-sets/IGVFDS1417TPKZ/), [IGVFDS9614JGLX](/measurement-sets/IGVFDS9614JGLX/), [IGVFDS0961NLGM](/measurement-sets/IGVFDS0961NLGM/), [IGVFDS4615AXMO](/measurement-sets/IGVFDS4615AXMO/) 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/IGVFDS4252LFRU/"
}
],
"INTERNAL_ACTION": [
{
"category": "mismatched status",
"detail": "Preview matrix file [IGVFFI3141VIGP](/matrix-files/IGVFFI3141VIGP/) 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/IGVFFI3141VIGP/"
},
{
"category": "mismatched status",
"detail": "Preview matrix file [IGVFFI8929UOQW](/matrix-files/IGVFFI8929UOQW/) 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/IGVFFI8929UOQW/"
},
{
"category": "mismatched status",
"detail": "Preview matrix file [IGVFFI8767IWEB](/matrix-files/IGVFFI8767IWEB/) 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/IGVFFI8767IWEB/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing file format specifications",
"detail": "Tabular file [IGVFFI4410YZQZ](/tabular-files/IGVFFI4410YZQZ/) 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/IGVFFI4410YZQZ/"
},
{
"category": "missing file format specifications",
"detail": "Tabular file [IGVFFI8786YBUA](/tabular-files/IGVFFI8786YBUA/) 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/IGVFFI8786YBUA/"
},
{
"category": "missing analysis step version",
"detail": "Analysis set [IGVFDS4252LFRU](/analysis-sets/IGVFDS4252LFRU/) links to file(s) [IGVFFI4410YZQZ](/tabular-files/IGVFFI4410YZQZ/), [IGVFFI8786YBUA](/tabular-files/IGVFFI8786YBUA/) 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/IGVFDS4252LFRU/"
},
{
"category": "missing derived from",
"detail": "Analysis set [IGVFDS4252LFRU](/analysis-sets/IGVFDS4252LFRU/) links to file(s) [IGVFFI3141VIGP](/matrix-files/IGVFFI3141VIGP/), [IGVFFI8767IWEB](/matrix-files/IGVFFI8767IWEB/), [IGVFFI8929UOQW](/matrix-files/IGVFFI8929UOQW/), [IGVFFI4410YZQZ](/tabular-files/IGVFFI4410YZQZ/), [IGVFFI8786YBUA](/tabular-files/IGVFFI8786YBUA/) 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/IGVFDS4252LFRU/"
}
]
},
"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"
},
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"creation_timestamp": "2024-12-04T20:07:37.878701+00:00",
"donors": [
{
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"aliases": [
"igvf:donor_of_WTC11"
],
"sex": "male",
"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": "2024-12-17T22:50:36.376287+00:00",
"file_format": "h5ad",
"file_size": 17240955988,
"href": "/matrix-files/IGVFFI3141VIGP/@@download/IGVFFI3141VIGP.h5ad",
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"upload_status": "validated"
},
{
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"accession": "IGVFFI8767IWEB",
"aliases": [
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],
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"creation_timestamp": "2024-12-17T23:44:11.744242+00:00",
"file_format": "hdf5",
"file_size": 673686640,
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"upload_status": "validated"
},
{
"@id": "/matrix-files/IGVFFI8929UOQW/",
"accession": "IGVFFI8929UOQW",
"aliases": [
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],
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"creation_timestamp": "2024-12-17T23:44:31.110178+00:00",
"file_format": "pkl",
"file_size": 2000717315,
"href": "/matrix-files/IGVFFI8929UOQW/@@download/IGVFFI8929UOQWpkl",
"s3_uri": "s3://igvf-files/2024/12/17/3205cd77-e2c7-48f6-858e-d7ff7d40509f/IGVFFI8929UOQWpkl",
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/s215194/Single_Cell/mini_cm_pilot_02_inducible/_435-438_WTC11_PB9/aggr_dataframe/aggr_combined_df_full.pkl",
"upload_status": "validated"
},
{
"@id": "/tabular-files/IGVFFI4410YZQZ/",
"accession": "IGVFFI4410YZQZ",
"aliases": [
"gary-hon:WTC11_CM_Pilot2_Mini_PB9_PrimaryAnalysis_DE_local"
],
"content_type": "unfiltered local differential expression",
"controlled_access": false,
"creation_timestamp": "2024-12-18T20:48:34.756501+00:00",
"file_format": "csv",
"file_size": 6592,
"href": "/tabular-files/IGVFFI4410YZQZ/@@download/IGVFFI4410YZQZ.csv.gz",
"s3_uri": "s3://igvf-files/2024/12/18/94cb8573-25f3-4a4d-bcc7-7b55f3002a56/IGVFFI4410YZQZ.csv.gz",
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"upload_status": "invalidated"
},
{
"@id": "/tabular-files/IGVFFI8786YBUA/",
"accession": "IGVFFI8786YBUA",
"aliases": [
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],
"content_type": "unfiltered global differential expression",
"controlled_access": false,
"creation_timestamp": "2024-12-18T20:48:48.810740+00:00",
"file_format": "csv",
"file_size": 382811,
"href": "/tabular-files/IGVFFI8786YBUA/@@download/IGVFFI8786YBUA.csv.gz",
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"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/s215194/IGVF/data_submission/reference_files/WTC11_CM_Pilot2_Mini_PB9_PrimaryAnalysis_DE_global.csv.gz",
"upload_status": "invalidated"
}
],
"functional_assay_mechanisms": [],
"input_file_sets": [
{
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"accession": "IGVFDS7818HFMO",
"aliases": [
"gary-hon:differentited_WTC11_CM_Pilot2_Mini_PB9_LW435"
],
"file_set_type": "experimental data",
"status": "preview"
},
{
"@id": "/auxiliary-sets/IGVFDS3881UZJT/",
"accession": "IGVFDS3881UZJT",
"aliases": [
"gary-hon:differentited_WTC11_CM_Pilot2_Mini_PB9_sgRNA_LW435"
],
"file_set_type": "gRNA sequencing",
"status": "preview"
},
{
"@id": "/auxiliary-sets/IGVFDS9289FWZN/",
"accession": "IGVFDS9289FWZN",
"aliases": [
"gary-hon:differentited_WTC11_CM_Pilot2_Mini_PB9_HTO_LW435"
],
"file_set_type": "cell hashing barcode sequencing",
"status": "preview"
},
{
"@id": "/measurement-sets/IGVFDS4615AXMO/",
"accession": "IGVFDS4615AXMO",
"aliases": [
"gary-hon:differentited_WTC11_CM_Pilot2_Mini_PB9_LW436"
],
"file_set_type": "experimental data",
"status": "preview"
},
{
"@id": "/auxiliary-sets/IGVFDS9781HZZV/",
"accession": "IGVFDS9781HZZV",
"aliases": [
"gary-hon:differentited_WTC11_CM_Pilot2_Mini_PB9_sgRNA_LW436"
],
"file_set_type": "gRNA sequencing",
"status": "preview"
},
{
"@id": "/auxiliary-sets/IGVFDS5210TKRS/",
"accession": "IGVFDS5210TKRS",
"aliases": [
"gary-hon:differentited_WTC11_CM_Pilot2_Mini_PB9_HTO_LW436"
],
"file_set_type": "cell hashing barcode sequencing",
"status": "preview"
},
{
"@id": "/measurement-sets/IGVFDS9614JGLX/",
"accession": "IGVFDS9614JGLX",
"aliases": [
"gary-hon:differentited_WTC11_CM_Pilot2_Mini_PB9_LW437"
],
"file_set_type": "experimental data",
"status": "preview"
},
{
"@id": "/auxiliary-sets/IGVFDS1417TPKZ/",
"accession": "IGVFDS1417TPKZ",
"aliases": [
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],
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"status": "preview"
},
{
"@id": "/auxiliary-sets/IGVFDS8878JVPZ/",
"accession": "IGVFDS8878JVPZ",
"aliases": [
"gary-hon:differentited_WTC11_CM_Pilot2_Mini_PB9_HTO_LW437"
],
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"status": "preview"
},
{
"@id": "/measurement-sets/IGVFDS0961NLGM/",
"accession": "IGVFDS0961NLGM",
"aliases": [
"gary-hon:differentited_WTC11_CM_Pilot2_Mini_PB9_LW438"
],
"file_set_type": "experimental data",
"status": "preview"
},
{
"@id": "/auxiliary-sets/IGVFDS0373CFJS/",
"accession": "IGVFDS0373CFJS",
"aliases": [
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],
"file_set_type": "gRNA sequencing",
"status": "preview"
},
{
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"accession": "IGVFDS3701EFIG",
"aliases": [
"gary-hon:differentited_WTC11_CM_Pilot2_Mini_PB9_HTO_LW438"
],
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"status": "preview"
}
],
"input_for": [],
"lab": {
"@id": "/labs/gary-hon/",
"title": "Gary Hon, UT"
},
"protocols": [
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],
"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/IGVFSM2176YXFG/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM2176YXFG",
"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": [
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],
"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_LW438), male, Homo sapiens modified with CRISPRi Sp-dCas9, transfected 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/IGVFSM8072YOLO/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM8072YOLO",
"aliases": [
"nikhil-munshi:differentited_WTC11_CM_Pilot2_Mini_PB9_LW437"
],
"classifications": [
"differentiated cell specimen"
],
"construct_library_sets": [
"/construct-library-sets/IGVFDS0346MQBH/"
],
"modifications": [
{
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"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_LW437), 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/IGVFSM8889XSOR/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM8889XSOR",
"aliases": [
"nikhil-munshi:differentited_WTC11_CM_Pilot2_Mini_PB9_LW436"
],
"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_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_LW436), 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/IGVFSM4418NJET/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM4418NJET",
"aliases": [
"nikhil-munshi:differentited_WTC11_CM_Pilot2_Mini_PB9_LW435"
],
"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_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_LW435), 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"
}
],
"schema_version": "9",
"status": "preview",
"submitted_by": {
"@id": "/users/b05645f1-2d56-4a5e-b272-4601e555a3fa/",
"title": "Mpathi Nzima"
},
"submitted_files_timestamp": "2024-12-17T22:50:36.376287+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": "51e138b8-6ad6-4bee-a743-3f3da05d4073",
"workflows": [
{
"@id": "/workflows/IGVFWF0190YALU/",
"accession": "IGVFWF0190YALU",
"name": "Hon Perturb-seq Workflow",
"status": "in progress",
"uniform_pipeline": false
}
]
}