{
"@context": "/terms/",
"@id": "/analysis-sets/IGVFDS7340YDHF/",
"@type": [
"AnalysisSet",
"FileSet",
"Item"
],
"accession": "IGVFDS7340YDHF",
"aliases": [
"gary-hon:WTC11_TF_Perturb_Seq_Pilot_iPSC_Lenti_PrimaryAnalysis"
],
"assay_titles": [
"Perturb-seq"
],
"audit": {
"ERROR": [
{
"category": "upload status not validated",
"detail": "Tabular file [IGVFFI5883SVNN](/tabular-files/IGVFFI5883SVNN/) has `upload_status` invalidated. Validation error detail: {\"md5sum\": \"original md5sum 92856ae7d73ef0fc07438a666cf24938 does not match newly calculated md5sum f46b358fe0c565d9a067694d7f084a98.\"}. Files are expected to be validated or validation exempted.",
"level": 60,
"level_name": "ERROR",
"name": "audit_upload_status",
"path": "/tabular-files/IGVFFI5883SVNN/"
},
{
"category": "unexpected input file set",
"detail": "Analysis set [IGVFDS7340YDHF](/analysis-sets/IGVFDS7340YDHF/) links to file set(s): [IGVFDS1931QVXR](/auxiliary-sets/IGVFDS1931QVXR/), [IGVFDS2692VBHQ](/measurement-sets/IGVFDS2692VBHQ/), [IGVFDS1937JPZI](/auxiliary-sets/IGVFDS1937JPZI/), [IGVFDS9718OGWQ](/auxiliary-sets/IGVFDS9718OGWQ/), [IGVFDS2373RGIJ](/auxiliary-sets/IGVFDS2373RGIJ/), [IGVFDS3975OFAO](/measurement-sets/IGVFDS3975OFAO/), [IGVFDS3495FUIW](/measurement-sets/IGVFDS3495FUIW/), [IGVFDS6503WNZT](/auxiliary-sets/IGVFDS6503WNZT/), [IGVFDS3465KEWH](/auxiliary-sets/IGVFDS3465KEWH/), [IGVFDS6015JDKU](/auxiliary-sets/IGVFDS6015JDKU/), [IGVFDS1128FXRR](/auxiliary-sets/IGVFDS1128FXRR/), [IGVFDS5429CXNB](/measurement-sets/IGVFDS5429CXNB/) 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/IGVFDS7340YDHF/"
},
{
"category": "upload status not validated",
"detail": "Tabular file [IGVFFI3020CFIL](/tabular-files/IGVFFI3020CFIL/) has `upload_status` invalidated. Validation error detail: {\"md5sum\": \"original md5sum 8661a38c51cacef5886db79cb4bd9b2b does not match newly calculated md5sum 468631d87c4079a4d3f16f8ef987209f.\"}. Files are expected to be validated or validation exempted.",
"level": 60,
"level_name": "ERROR",
"name": "audit_upload_status",
"path": "/tabular-files/IGVFFI3020CFIL/"
}
],
"INTERNAL_ACTION": [
{
"category": "mismatched status",
"detail": "Preview matrix file [IGVFFI5102YSIV](/matrix-files/IGVFFI5102YSIV/) 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/IGVFFI5102YSIV/"
},
{
"category": "mismatched status",
"detail": "Preview matrix file [IGVFFI4463LVNM](/matrix-files/IGVFFI4463LVNM/) 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/IGVFFI4463LVNM/"
},
{
"category": "mismatched status",
"detail": "Preview matrix file [IGVFFI7586HWIH](/matrix-files/IGVFFI7586HWIH/) 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/IGVFFI7586HWIH/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing file format specifications",
"detail": "Tabular file [IGVFFI5883SVNN](/tabular-files/IGVFFI5883SVNN/) 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/IGVFFI5883SVNN/"
},
{
"category": "missing analysis step version",
"detail": "Analysis set [IGVFDS7340YDHF](/analysis-sets/IGVFDS7340YDHF/) links to file(s) [IGVFFI3020CFIL](/tabular-files/IGVFFI3020CFIL/), [IGVFFI5883SVNN](/tabular-files/IGVFFI5883SVNN/) 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/IGVFDS7340YDHF/"
},
{
"category": "missing derived from",
"detail": "Analysis set [IGVFDS7340YDHF](/analysis-sets/IGVFDS7340YDHF/) links to file(s) [IGVFFI4463LVNM](/matrix-files/IGVFFI4463LVNM/), [IGVFFI7586HWIH](/matrix-files/IGVFFI7586HWIH/), [IGVFFI5102YSIV](/matrix-files/IGVFFI5102YSIV/), [IGVFFI3020CFIL](/tabular-files/IGVFFI3020CFIL/), [IGVFFI5883SVNN](/tabular-files/IGVFFI5883SVNN/) 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/IGVFDS7340YDHF/"
},
{
"category": "missing file format specifications",
"detail": "Tabular file [IGVFFI3020CFIL](/tabular-files/IGVFFI3020CFIL/) 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/IGVFFI3020CFIL/"
}
]
},
"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": "2024-12-04T20:07:15.325181+00:00",
"donors": [
{
"@id": "/human-donors/IGVFDO1756PPKO/",
"accession": "IGVFDO1756PPKO",
"aliases": [
"igvf:donor_of_WTC11"
],
"sex": "male",
"status": "released",
"taxa": "Homo sapiens"
}
],
"file_set_type": "principal analysis",
"files": [
{
"@id": "/matrix-files/IGVFFI4463LVNM/",
"accession": "IGVFFI4463LVNM",
"aliases": [
"gary-hon:WTC11_TF_Perturb_Seq_Pilot_iPSC_Lenti_PrimaryAnalysis_h5ad"
],
"content_type": "sparse gene count matrix",
"creation_timestamp": "2024-12-17T22:37:26.749555+00:00",
"file_format": "h5ad",
"file_size": 18523461231,
"href": "/matrix-files/IGVFFI4463LVNM/@@download/IGVFFI4463LVNM.h5ad",
"s3_uri": "s3://igvf-files/2024/12/17/85629622-1e47-41a9-8721-b13ff8d078ca/IGVFFI4463LVNM.h5ad",
"status": "preview",
"submitted_file_name": "/project/shared/gcrb_igvf/data/shared/TF_Perturbseq_pilot/H5AD/V0.1_TF_Perturbseq_pilot_sgRNACells_filtered_w_embedding_full_ipsc_reprocessed.h5ad",
"upload_status": "validated"
},
{
"@id": "/matrix-files/IGVFFI7586HWIH/",
"accession": "IGVFFI7586HWIH",
"aliases": [
"gary-hon:WTC11_TF_Perturb_Seq_Pilot_iPSC_Lenti_PrimaryAnalysis_h5"
],
"content_type": "filtered feature barcode matrix",
"creation_timestamp": "2024-12-17T23:40:29.786979+00:00",
"file_format": "hdf5",
"file_size": 428983756,
"href": "/matrix-files/IGVFFI7586HWIH/@@download/IGVFFI7586HWIH.h5",
"s3_uri": "s3://igvf-files/2024/12/17/b9815896-8cc7-4e7c-9b25-48e50f636ca2/IGVFFI7586HWIH.h5",
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/s215194/Single_Cell/TF_perturb_seq/_pipeline_reporcessing/_combined_ipsc/aggr_transciptome/TF_perturbseq_ipsc/outs/count/filtered_feature_bc_matrix.h5",
"upload_status": "validated"
},
{
"@id": "/matrix-files/IGVFFI5102YSIV/",
"accession": "IGVFFI5102YSIV",
"aliases": [
"gary-hon:WTC11_TF_Perturb_Seq_Pilot_iPSC_Lenti_PrimaryAnalysis_pkl"
],
"content_type": "raw feature barcode matrix",
"creation_timestamp": "2024-12-17T23:40:42.525063+00:00",
"file_format": "pkl",
"file_size": 588814134,
"href": "/matrix-files/IGVFFI5102YSIV/@@download/IGVFFI5102YSIVpkl",
"s3_uri": "s3://igvf-files/2024/12/17/92d162a1-dbe0-48af-a349-e99be61ac1f7/IGVFFI5102YSIVpkl",
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/s215194/Single_Cell/TF_perturb_seq/_pipeline_reporcessing/_combined_ipsc/aggr_dataframe/aggr_combined_df_full.pkl",
"upload_status": "validated"
},
{
"@id": "/tabular-files/IGVFFI3020CFIL/",
"accession": "IGVFFI3020CFIL",
"aliases": [
"gary-hon:WTC11_TF_Perturb_Seq_Pilot_iPSC_Lenti_PrimaryAnalysis_DE_local"
],
"content_type": "unfiltered local differential expression",
"controlled_access": false,
"creation_timestamp": "2024-12-18T19:31:10.320317+00:00",
"file_format": "csv",
"file_size": 3129,
"href": "/tabular-files/IGVFFI3020CFIL/@@download/IGVFFI3020CFIL.csv.gz",
"s3_uri": "s3://igvf-files/2024/12/18/a5575269-979b-406f-acaa-707db71d447c/IGVFFI3020CFIL.csv.gz",
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/s215194/IGVF/data_submission/reference_files/WTC11_TF_Perturb_Seq_Pilot_iPSC_Lenti_PrimaryAnalysis_DE_local.csv.gz",
"upload_status": "invalidated"
},
{
"@id": "/tabular-files/IGVFFI5883SVNN/",
"accession": "IGVFFI5883SVNN",
"aliases": [
"gary-hon:WTC11_TF_Perturb_Seq_Pilot_iPSC_Lenti_PrimaryAnalysis_DE_global"
],
"content_type": "unfiltered global differential expression",
"controlled_access": false,
"creation_timestamp": "2024-12-18T19:31:18.220958+00:00",
"file_format": "csv",
"file_size": 288219,
"href": "/tabular-files/IGVFFI5883SVNN/@@download/IGVFFI5883SVNN.csv.gz",
"s3_uri": "s3://igvf-files/2024/12/18/690c0b30-08b4-4014-b95e-dc952c50e35b/IGVFFI5883SVNN.csv.gz",
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/s215194/IGVF/data_submission/reference_files/WTC11_TF_Perturb_Seq_Pilot_iPSC_Lenti_PrimaryAnalysis_DE_global.csv.gz",
"upload_status": "invalidated"
}
],
"functional_assay_mechanisms": [],
"input_file_sets": [
{
"@id": "/measurement-sets/IGVFDS5429CXNB/",
"accession": "IGVFDS5429CXNB",
"aliases": [
"gary-hon:TF_Perturb_Seq_Pilot_Lenti_iPSC_LW286"
],
"file_set_type": "experimental data",
"status": "preview"
},
{
"@id": "/auxiliary-sets/IGVFDS1128FXRR/",
"accession": "IGVFDS1128FXRR",
"aliases": [
"gary-hon:TF_Perturb_Seq_Pilot_Lenti_iPSC_sgRNA_LW286"
],
"file_set_type": "gRNA sequencing",
"status": "preview"
},
{
"@id": "/auxiliary-sets/IGVFDS3465KEWH/",
"accession": "IGVFDS3465KEWH",
"aliases": [
"gary-hon:TF_Perturb_Seq_Pilot_Lenti_iPSC_HTO_LW286"
],
"file_set_type": "cell hashing barcode sequencing",
"status": "preview"
},
{
"@id": "/measurement-sets/IGVFDS2692VBHQ/",
"accession": "IGVFDS2692VBHQ",
"aliases": [
"gary-hon:TF_Perturb_Seq_Pilot_Lenti_iPSC_LW287"
],
"file_set_type": "experimental data",
"status": "preview"
},
{
"@id": "/auxiliary-sets/IGVFDS1937JPZI/",
"accession": "IGVFDS1937JPZI",
"aliases": [
"gary-hon:TF_Perturb_Seq_Pilot_Lenti_iPSC_sgRNA_LW287"
],
"file_set_type": "gRNA sequencing",
"status": "preview"
},
{
"@id": "/auxiliary-sets/IGVFDS2373RGIJ/",
"accession": "IGVFDS2373RGIJ",
"aliases": [
"gary-hon:TF_Perturb_Seq_Pilot_Lenti_iPSC_HTO_LW287"
],
"file_set_type": "cell hashing barcode sequencing",
"status": "preview"
},
{
"@id": "/measurement-sets/IGVFDS3975OFAO/",
"accession": "IGVFDS3975OFAO",
"aliases": [
"gary-hon:TF_Perturb_Seq_Pilot_Lenti_iPSC_LW288"
],
"file_set_type": "experimental data",
"status": "preview"
},
{
"@id": "/auxiliary-sets/IGVFDS6503WNZT/",
"accession": "IGVFDS6503WNZT",
"aliases": [
"gary-hon:TF_Perturb_Seq_Pilot_Lenti_iPSC_sgRNA_LW288"
],
"file_set_type": "gRNA sequencing",
"status": "preview"
},
{
"@id": "/auxiliary-sets/IGVFDS9718OGWQ/",
"accession": "IGVFDS9718OGWQ",
"aliases": [
"gary-hon:TF_Perturb_Seq_Pilot_Lenti_iPSC_HTO_LW288"
],
"file_set_type": "cell hashing barcode sequencing",
"status": "preview"
},
{
"@id": "/measurement-sets/IGVFDS3495FUIW/",
"accession": "IGVFDS3495FUIW",
"aliases": [
"gary-hon:TF_Perturb_Seq_Pilot_Lenti_iPSC_LW289"
],
"file_set_type": "experimental data",
"status": "preview"
},
{
"@id": "/auxiliary-sets/IGVFDS1931QVXR/",
"accession": "IGVFDS1931QVXR",
"aliases": [
"gary-hon:TF_Perturb_Seq_Pilot_Lenti_iPSC_sgRNA_LW289"
],
"file_set_type": "gRNA sequencing",
"status": "preview"
},
{
"@id": "/auxiliary-sets/IGVFDS6015JDKU/",
"accession": "IGVFDS6015JDKU",
"aliases": [
"gary-hon:TF_Perturb_Seq_Pilot_Lenti_iPSC_HTO_LW289"
],
"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": "GM25256 (WTC-11) cell line, modified with CRISPR modifications, transfected with a guide library",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM1597KVRS/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM1597KVRS",
"aliases": [
"nikhil-munshi:differentited_WTC11_TF_Perturb_Seq_Pilot_iPSC_Lenti_LW289"
],
"classifications": [
"cell line"
],
"construct_library_sets": [
"/construct-library-sets/IGVFDS2302LCEO/"
],
"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) cell line (cellular sub pool: subpool_LW289), male, Homo sapiens modified with CRISPRi Sp-dCas9, transduced (lentivirus) with a guide library",
"taxa": "Homo sapiens"
},
{
"@id": "/in-vitro-systems/IGVFSM2726ORRN/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM2726ORRN",
"aliases": [
"nikhil-munshi:differentited_WTC11_TF_Perturb_Seq_Pilot_iPSC_Lenti_LW286"
],
"classifications": [
"cell line"
],
"construct_library_sets": [
"/construct-library-sets/IGVFDS2302LCEO/"
],
"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) cell line (cellular sub pool: subpool_LW286), male, Homo sapiens modified with CRISPRi Sp-dCas9, transduced (lentivirus) with a guide library",
"taxa": "Homo sapiens"
},
{
"@id": "/in-vitro-systems/IGVFSM1153INDY/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM1153INDY",
"aliases": [
"nikhil-munshi:differentited_WTC11_TF_Perturb_Seq_Pilot_iPSC_Lenti_LW287"
],
"classifications": [
"cell line"
],
"construct_library_sets": [
"/construct-library-sets/IGVFDS2302LCEO/"
],
"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) cell line (cellular sub pool: subpool_LW287), male, Homo sapiens modified with CRISPRi Sp-dCas9, transduced (lentivirus) with a guide library",
"taxa": "Homo sapiens"
},
{
"@id": "/in-vitro-systems/IGVFSM9411HZLU/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM9411HZLU",
"aliases": [
"nikhil-munshi:differentited_WTC11_TF_Perturb_Seq_Pilot_iPSC_Lenti_LW288"
],
"classifications": [
"cell line"
],
"construct_library_sets": [
"/construct-library-sets/IGVFDS2302LCEO/"
],
"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) cell line (cellular sub pool: subpool_LW288), male, Homo sapiens modified with CRISPRi Sp-dCas9, transduced (lentivirus) with a guide library",
"taxa": "Homo sapiens"
}
],
"schema_version": "9",
"status": "preview",
"submitted_by": {
"@id": "/users/b05645f1-2d56-4a5e-b272-4601e555a3fa/",
"title": "Mpathi Nzima"
},
"submitted_files_timestamp": "2024-12-17T22:37:26.749555+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": "ab709a68-2d95-46ba-9462-decc91623d62",
"workflows": [
{
"@id": "/workflows/IGVFWF0190YALU/",
"accession": "IGVFWF0190YALU",
"name": "Hon Perturb-seq Workflow",
"status": "in progress",
"uniform_pipeline": false
}
]
}