{
"@context": "/terms/",
"@id": "/analysis-sets/IGVFDS2266YDVM/",
"@type": [
"AnalysisSet",
"FileSet",
"Item"
],
"accession": "IGVFDS2266YDVM",
"aliases": [
"gary-hon:H9_CM_Pilot2_Mini_PB9_PrimaryAnalysis"
],
"assay_titles": [
"Perturb-seq"
],
"audit": {
"ERROR": [
{
"category": "unexpected input file set",
"detail": "Analysis set [IGVFDS2266YDVM](/analysis-sets/IGVFDS2266YDVM/) links to file set(s): [IGVFDS5403GYDH](/auxiliary-sets/IGVFDS5403GYDH/), [IGVFDS1340IBKW](/auxiliary-sets/IGVFDS1340IBKW/), [IGVFDS8183DTKY](/measurement-sets/IGVFDS8183DTKY/), [IGVFDS1182KBMU](/auxiliary-sets/IGVFDS1182KBMU/), [IGVFDS2275IPCJ](/auxiliary-sets/IGVFDS2275IPCJ/), [IGVFDS8751LXWJ](/measurement-sets/IGVFDS8751LXWJ/), [IGVFDS6475OLUM](/auxiliary-sets/IGVFDS6475OLUM/), [IGVFDS7288IQLC](/measurement-sets/IGVFDS7288IQLC/), [IGVFDS3919NBFE](/auxiliary-sets/IGVFDS3919NBFE/), [IGVFDS5502LTCL](/measurement-sets/IGVFDS5502LTCL/), [IGVFDS0785CQUX](/auxiliary-sets/IGVFDS0785CQUX/), [IGVFDS3774FYIW](/auxiliary-sets/IGVFDS3774FYIW/) 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/IGVFDS2266YDVM/"
},
{
"category": "upload status not validated",
"detail": "Tabular file [IGVFFI1867ROFS](/tabular-files/IGVFFI1867ROFS/) has `upload_status` invalidated. Validation error detail: {\"md5sum\": \"original md5sum 808b1e9a7f146376437acda477b4431d does not match newly calculated md5sum 8000063afa1312cd17c3cb3db550b32f.\"}. Files are expected to be validated or validation exempted.",
"level": 60,
"level_name": "ERROR",
"name": "audit_upload_status",
"path": "/tabular-files/IGVFFI1867ROFS/"
},
{
"category": "upload status not validated",
"detail": "Tabular file [IGVFFI8753JHNH](/tabular-files/IGVFFI8753JHNH/) has `upload_status` invalidated. Validation error detail: {\"md5sum\": \"original md5sum 5c4b4d4cc503658025fcd6ca2cb8fba6 does not match newly calculated md5sum a19b65f2011b45b4d15bbc54de2b6a70.\"}. Files are expected to be validated or validation exempted.",
"level": 60,
"level_name": "ERROR",
"name": "audit_upload_status",
"path": "/tabular-files/IGVFFI8753JHNH/"
}
],
"INTERNAL_ACTION": [
{
"category": "mismatched status",
"detail": "Preview matrix file [IGVFFI6483VROG](/matrix-files/IGVFFI6483VROG/) 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/IGVFFI6483VROG/"
},
{
"category": "mismatched status",
"detail": "Preview matrix file [IGVFFI5815NBHE](/matrix-files/IGVFFI5815NBHE/) 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/IGVFFI5815NBHE/"
},
{
"category": "mismatched status",
"detail": "Preview matrix file [IGVFFI1539OEIK](/matrix-files/IGVFFI1539OEIK/) 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/IGVFFI1539OEIK/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing analysis step version",
"detail": "Analysis set [IGVFDS2266YDVM](/analysis-sets/IGVFDS2266YDVM/) links to file(s) [IGVFFI8753JHNH](/tabular-files/IGVFFI8753JHNH/), [IGVFFI1867ROFS](/tabular-files/IGVFFI1867ROFS/) 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/IGVFDS2266YDVM/"
},
{
"category": "missing derived from",
"detail": "Analysis set [IGVFDS2266YDVM](/analysis-sets/IGVFDS2266YDVM/) links to file(s) [IGVFFI6483VROG](/matrix-files/IGVFFI6483VROG/), [IGVFFI1539OEIK](/matrix-files/IGVFFI1539OEIK/), [IGVFFI5815NBHE](/matrix-files/IGVFFI5815NBHE/), [IGVFFI8753JHNH](/tabular-files/IGVFFI8753JHNH/), [IGVFFI1867ROFS](/tabular-files/IGVFFI1867ROFS/) 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/IGVFDS2266YDVM/"
},
{
"category": "missing file format specifications",
"detail": "Tabular file [IGVFFI1867ROFS](/tabular-files/IGVFFI1867ROFS/) 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/IGVFFI1867ROFS/"
},
{
"category": "missing file format specifications",
"detail": "Tabular file [IGVFFI8753JHNH](/tabular-files/IGVFFI8753JHNH/) 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/IGVFFI8753JHNH/"
}
]
},
"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": "2024-12-04T20:07:34.656354+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/IGVFFI6483VROG/",
"accession": "IGVFFI6483VROG",
"aliases": [
"gary-hon:H9_CM_Pilot2_Mini_PB9_PrimaryAnalysis_h5ad"
],
"content_type": "sparse gene count matrix",
"creation_timestamp": "2024-12-17T22:47:39.541942+00:00",
"file_format": "h5ad",
"file_size": 18825207540,
"href": "/matrix-files/IGVFFI6483VROG/@@download/IGVFFI6483VROG.h5ad",
"s3_uri": "s3://igvf-files/2024/12/17/98195f6d-bb09-4ade-bf51-43aec1ee6ced/IGVFFI6483VROG.h5ad",
"status": "preview",
"submitted_file_name": "/project/shared/gcrb_igvf/data/shared/mini_cm_pilot02_PB9/H5AD/V0._mini_cm02_H9_PB9_sgRNACells_filtered_w_embedding.h5ad",
"upload_status": "validated"
},
{
"@id": "/matrix-files/IGVFFI1539OEIK/",
"accession": "IGVFFI1539OEIK",
"aliases": [
"gary-hon:H9_CM_Pilot2_Mini_PB9_PrimaryAnalysis_h5"
],
"content_type": "filtered feature barcode matrix",
"creation_timestamp": "2024-12-17T23:43:18.772479+00:00",
"file_format": "hdf5",
"file_size": 667371297,
"href": "/matrix-files/IGVFFI1539OEIK/@@download/IGVFFI1539OEIK.h5",
"s3_uri": "s3://igvf-files/2024/12/17/0325499e-338d-4d5d-8564-ef943a4e44fe/IGVFFI1539OEIK.h5",
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/s215194/Single_Cell/mini_cm_pilot_02_inducible/_431_434_H9_PB9/_aggr_transcriptome/cm_pilot_mini_02_no_normalization_H9_PB9/outs/count/filtered_feature_bc_matrix.h5",
"upload_status": "validated"
},
{
"@id": "/matrix-files/IGVFFI5815NBHE/",
"accession": "IGVFFI5815NBHE",
"aliases": [
"gary-hon:H9_CM_Pilot2_Mini_PB9_PrimaryAnalysis_pkl"
],
"content_type": "raw feature barcode matrix",
"creation_timestamp": "2024-12-17T23:43:38.946141+00:00",
"file_format": "pkl",
"file_size": 2159941743,
"href": "/matrix-files/IGVFFI5815NBHE/@@download/IGVFFI5815NBHEpkl",
"s3_uri": "s3://igvf-files/2024/12/17/7005f296-49b6-4585-a872-1a33551558eb/IGVFFI5815NBHEpkl",
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/s215194/Single_Cell/mini_cm_pilot_02_inducible/_431_434_H9_PB9/aggr_dataframe/aggr_combined_df_full.pkl",
"upload_status": "validated"
},
{
"@id": "/tabular-files/IGVFFI8753JHNH/",
"accession": "IGVFFI8753JHNH",
"aliases": [
"gary-hon:H9_CM_Pilot2_Mini_PB9_PrimaryAnalysis_DE_local"
],
"content_type": "unfiltered local differential expression",
"controlled_access": false,
"creation_timestamp": "2024-12-18T20:48:04.760181+00:00",
"file_format": "csv",
"file_size": 6817,
"href": "/tabular-files/IGVFFI8753JHNH/@@download/IGVFFI8753JHNH.csv.gz",
"s3_uri": "s3://igvf-files/2024/12/18/dea5b153-2f6d-46ec-97b9-c7497be75c63/IGVFFI8753JHNH.csv.gz",
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/s215194/IGVF/data_submission/reference_files/H9_CM_Pilot2_Mini_PB9_PrimaryAnalysis_DE_local.csv.gz",
"upload_status": "invalidated"
},
{
"@id": "/tabular-files/IGVFFI1867ROFS/",
"accession": "IGVFFI1867ROFS",
"aliases": [
"gary-hon:H9_CM_Pilot2_Mini_PB9_PrimaryAnalysis_DE_global"
],
"content_type": "unfiltered global differential expression",
"controlled_access": false,
"creation_timestamp": "2024-12-18T20:48:20.349603+00:00",
"file_format": "csv",
"file_size": 1545525,
"href": "/tabular-files/IGVFFI1867ROFS/@@download/IGVFFI1867ROFS.csv.gz",
"s3_uri": "s3://igvf-files/2024/12/18/9dfb6e0f-fd12-4f55-9f9c-5edce46702eb/IGVFFI1867ROFS.csv.gz",
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/s215194/IGVF/data_submission/reference_files/H9_CM_Pilot2_Mini_PB9_PrimaryAnalysis_DE_global.csv.gz",
"upload_status": "invalidated"
}
],
"functional_assay_mechanisms": [],
"input_file_sets": [
{
"@id": "/measurement-sets/IGVFDS5502LTCL/",
"accession": "IGVFDS5502LTCL",
"aliases": [
"gary-hon:differentited_H9_CM_Pilot2_Mini_PB9_LW431"
],
"file_set_type": "experimental data",
"status": "preview"
},
{
"@id": "/auxiliary-sets/IGVFDS1182KBMU/",
"accession": "IGVFDS1182KBMU",
"aliases": [
"gary-hon:differentited_H9_CM_Pilot2_Mini_PB9_sgRNA_LW431"
],
"file_set_type": "gRNA sequencing",
"status": "preview"
},
{
"@id": "/auxiliary-sets/IGVFDS2275IPCJ/",
"accession": "IGVFDS2275IPCJ",
"aliases": [
"gary-hon:differentited_H9_CM_Pilot2_Mini_PB9_HTO_LW431"
],
"file_set_type": "cell hashing barcode sequencing",
"status": "preview"
},
{
"@id": "/measurement-sets/IGVFDS8183DTKY/",
"accession": "IGVFDS8183DTKY",
"aliases": [
"gary-hon:differentited_H9_CM_Pilot2_Mini_PB9_LW432"
],
"file_set_type": "experimental data",
"status": "preview"
},
{
"@id": "/auxiliary-sets/IGVFDS5403GYDH/",
"accession": "IGVFDS5403GYDH",
"aliases": [
"gary-hon:differentited_H9_CM_Pilot2_Mini_PB9_sgRNA_LW432"
],
"file_set_type": "gRNA sequencing",
"status": "preview"
},
{
"@id": "/auxiliary-sets/IGVFDS6475OLUM/",
"accession": "IGVFDS6475OLUM",
"aliases": [
"gary-hon:differentited_H9_CM_Pilot2_Mini_PB9_HTO_LW432"
],
"file_set_type": "cell hashing barcode sequencing",
"status": "preview"
},
{
"@id": "/measurement-sets/IGVFDS8751LXWJ/",
"accession": "IGVFDS8751LXWJ",
"aliases": [
"gary-hon:differentited_H9_CM_Pilot2_Mini_PB9_LW433"
],
"file_set_type": "experimental data",
"status": "preview"
},
{
"@id": "/auxiliary-sets/IGVFDS3919NBFE/",
"accession": "IGVFDS3919NBFE",
"aliases": [
"gary-hon:differentited_H9_CM_Pilot2_Mini_PB9_sgRNA_LW433"
],
"file_set_type": "gRNA sequencing",
"status": "preview"
},
{
"@id": "/auxiliary-sets/IGVFDS3774FYIW/",
"accession": "IGVFDS3774FYIW",
"aliases": [
"gary-hon:differentited_H9_CM_Pilot2_Mini_PB9_HTO_LW433"
],
"file_set_type": "cell hashing barcode sequencing",
"status": "preview"
},
{
"@id": "/measurement-sets/IGVFDS7288IQLC/",
"accession": "IGVFDS7288IQLC",
"aliases": [
"gary-hon:differentited_H9_CM_Pilot2_Mini_PB9_LW434"
],
"file_set_type": "experimental data",
"status": "preview"
},
{
"@id": "/auxiliary-sets/IGVFDS0785CQUX/",
"accession": "IGVFDS0785CQUX",
"aliases": [
"gary-hon:differentited_H9_CM_Pilot2_Mini_PB9_sgRNA_LW434"
],
"file_set_type": "gRNA sequencing",
"status": "preview"
},
{
"@id": "/auxiliary-sets/IGVFDS1340IBKW/",
"accession": "IGVFDS1340IBKW",
"aliases": [
"gary-hon:differentited_H9_CM_Pilot2_Mini_PB9_HTO_LW434"
],
"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/IGVFSM8133YEXK/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM8133YEXK",
"aliases": [
"nikhil-munshi:differentited_H9_CM_Pilot2_Mini_PB9_LW434"
],
"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_LW434), 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/IGVFSM5829AVCL/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM5829AVCL",
"aliases": [
"nikhil-munshi:differentited_H9_CM_Pilot2_Mini_PB9_LW431"
],
"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_LW431), 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/IGVFSM3839SOTK/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM3839SOTK",
"aliases": [
"nikhil-munshi:differentited_H9_CM_Pilot2_Mini_PB9_LW432"
],
"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_LW432), 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/IGVFSM1513DHGW/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM1513DHGW",
"aliases": [
"nikhil-munshi:differentited_H9_CM_Pilot2_Mini_PB9_LW433"
],
"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_LW433), 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": "2024-12-17T22:47:39.541942+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": "9459771b-9580-4cf8-9ca5-757bc9a1f303",
"workflows": [
{
"@id": "/workflows/IGVFWF0190YALU/",
"accession": "IGVFWF0190YALU",
"name": "Hon Perturb-seq Workflow",
"status": "in progress",
"uniform_pipeline": false
}
]
}