{
"@context": "/terms/",
"@id": "/analysis-sets/IGVFDS4389OUWU/",
"@type": [
"AnalysisSet",
"FileSet",
"Item"
],
"accession": "IGVFDS4389OUWU",
"aliases": [
"gary-hon:TF_Perturb_Seq_Pilot_Lenti_CM_PrimaryAnalysis"
],
"assay_titles": [
"Perturb-seq"
],
"audit": {
"ERROR": [
{
"category": "unexpected input file set",
"detail": "Analysis set [IGVFDS4389OUWU](/analysis-sets/IGVFDS4389OUWU/) links to file set(s): [IGVFDS0109SCQO](/auxiliary-sets/IGVFDS0109SCQO/), [IGVFDS8280AMDA](/auxiliary-sets/IGVFDS8280AMDA/), [IGVFDS4852MAUM](/measurement-sets/IGVFDS4852MAUM/), [IGVFDS8139DLEM](/auxiliary-sets/IGVFDS8139DLEM/), [IGVFDS0997MTQA](/auxiliary-sets/IGVFDS0997MTQA/), [IGVFDS7834BXBN](/measurement-sets/IGVFDS7834BXBN/), [IGVFDS6861GRJI](/auxiliary-sets/IGVFDS6861GRJI/), [IGVFDS2628PYOH](/measurement-sets/IGVFDS2628PYOH/), [IGVFDS5228AHGR](/auxiliary-sets/IGVFDS5228AHGR/), [IGVFDS7027VRZT](/auxiliary-sets/IGVFDS7027VRZT/), [IGVFDS6231TYIS](/auxiliary-sets/IGVFDS6231TYIS/), [IGVFDS7733OTCA](/measurement-sets/IGVFDS7733OTCA/) 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/IGVFDS4389OUWU/"
},
{
"category": "upload status not validated",
"detail": "Tabular file [IGVFFI7266NWTF](/tabular-files/IGVFFI7266NWTF/) has `upload_status` invalidated. Validation error detail: {\"md5sum\": \"original md5sum 23d62647cc9df0a877a876b3b4a42f3f does not match newly calculated md5sum 96e36a0282823b2127cb6d119c5fa7e4.\"}. Files are expected to be validated or validation exempted.",
"level": 60,
"level_name": "ERROR",
"name": "audit_upload_status",
"path": "/tabular-files/IGVFFI7266NWTF/"
},
{
"category": "upload status not validated",
"detail": "Tabular file [IGVFFI4818IAJW](/tabular-files/IGVFFI4818IAJW/) has `upload_status` invalidated. Validation error detail: {\"md5sum\": \"original md5sum b3204244c4d15daf18f7ab6134f3e35c does not match newly calculated md5sum 978542c9bae8ae009257e9e42aea5576.\"}. Files are expected to be validated or validation exempted.",
"level": 60,
"level_name": "ERROR",
"name": "audit_upload_status",
"path": "/tabular-files/IGVFFI4818IAJW/"
}
],
"INTERNAL_ACTION": [
{
"category": "mismatched status",
"detail": "Preview matrix file [IGVFFI5769PLGK](/matrix-files/IGVFFI5769PLGK/) 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/IGVFFI5769PLGK/"
},
{
"category": "mismatched status",
"detail": "Preview matrix file [IGVFFI4195JWSH](/matrix-files/IGVFFI4195JWSH/) 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/IGVFFI4195JWSH/"
},
{
"category": "mismatched status",
"detail": "Preview matrix file [IGVFFI3549MTZZ](/matrix-files/IGVFFI3549MTZZ/) 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/IGVFFI3549MTZZ/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing analysis step version",
"detail": "Analysis set [IGVFDS4389OUWU](/analysis-sets/IGVFDS4389OUWU/) links to file(s) [IGVFFI7266NWTF](/tabular-files/IGVFFI7266NWTF/), [IGVFFI4818IAJW](/tabular-files/IGVFFI4818IAJW/) 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/IGVFDS4389OUWU/"
},
{
"category": "missing derived from",
"detail": "Analysis set [IGVFDS4389OUWU](/analysis-sets/IGVFDS4389OUWU/) links to file(s) [IGVFFI4195JWSH](/matrix-files/IGVFFI4195JWSH/), [IGVFFI3549MTZZ](/matrix-files/IGVFFI3549MTZZ/), [IGVFFI5769PLGK](/matrix-files/IGVFFI5769PLGK/), [IGVFFI7266NWTF](/tabular-files/IGVFFI7266NWTF/), [IGVFFI4818IAJW](/tabular-files/IGVFFI4818IAJW/) 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/IGVFDS4389OUWU/"
},
{
"category": "missing file format specifications",
"detail": "Tabular file [IGVFFI7266NWTF](/tabular-files/IGVFFI7266NWTF/) 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/IGVFFI7266NWTF/"
},
{
"category": "missing file format specifications",
"detail": "Tabular file [IGVFFI4818IAJW](/tabular-files/IGVFFI4818IAJW/) 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/IGVFFI4818IAJW/"
}
]
},
"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": "2024-05-10T17:37:51.579901+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/IGVFFI4195JWSH/",
"accession": "IGVFFI4195JWSH",
"aliases": [
"gary-hon:TF_Perturb_Seq_Pilot_Lenti_CM_PrimaryAnalysis_h5ad"
],
"content_type": "sparse gene count matrix",
"creation_timestamp": "2024-12-17T22:32:29.309598+00:00",
"file_format": "h5ad",
"file_size": 12885272929,
"href": "/matrix-files/IGVFFI4195JWSH/@@download/IGVFFI4195JWSH.h5ad",
"s3_uri": "s3://igvf-files/2024/12/17/37171186-765a-4fb5-8fc7-d02e9e67025c/IGVFFI4195JWSH.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_cm_reprocessed.h5ad",
"upload_status": "validated"
},
{
"@id": "/matrix-files/IGVFFI3549MTZZ/",
"accession": "IGVFFI3549MTZZ",
"aliases": [
"gary-hon:TF_Perturb_Seq_Pilot_Lenti_CM_PrimaryAnalysis_h5"
],
"content_type": "filtered feature barcode matrix",
"creation_timestamp": "2024-12-17T23:39:31.221402+00:00",
"file_format": "hdf5",
"file_size": 448440774,
"href": "/matrix-files/IGVFFI3549MTZZ/@@download/IGVFFI3549MTZZ.h5",
"s3_uri": "s3://igvf-files/2024/12/17/0833527a-34ee-4ef7-86e4-3d5dbed2b5bb/IGVFFI3549MTZZ.h5",
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/s215194/Single_Cell/TF_perturb_seq/_pipeline_reporcessing/_combined_cm/aggr_transciptome/TF_perturbseq_CM/outs/count/filtered_feature_bc_matrix.h5",
"upload_status": "validated"
},
{
"@id": "/matrix-files/IGVFFI5769PLGK/",
"accession": "IGVFFI5769PLGK",
"aliases": [
"gary-hon:TF_Perturb_Seq_Pilot_Lenti_CM_PrimaryAnalysis_pkl"
],
"content_type": "raw feature barcode matrix",
"creation_timestamp": "2024-12-17T23:39:44.883838+00:00",
"file_format": "pkl",
"file_size": 394516172,
"href": "/matrix-files/IGVFFI5769PLGK/@@download/IGVFFI5769PLGKpkl",
"s3_uri": "s3://igvf-files/2024/12/17/8c73b4d9-ef4e-4c1b-9d79-e7a81b51e04d/IGVFFI5769PLGKpkl",
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/s215194/Single_Cell/TF_perturb_seq/_pipeline_reporcessing/_combined_cm/aggr_dataframe/aggr_combined_df_full.pkl",
"upload_status": "validated"
},
{
"@id": "/tabular-files/IGVFFI7266NWTF/",
"accession": "IGVFFI7266NWTF",
"aliases": [
"gary-hon:TF_Perturb_Seq_Pilot_Lenti_CM_PrimaryAnalysis_DE_global"
],
"content_type": "unfiltered global differential expression",
"controlled_access": false,
"creation_timestamp": "2024-12-18T19:31:00.840167+00:00",
"file_format": "csv",
"file_size": 733520,
"href": "/tabular-files/IGVFFI7266NWTF/@@download/IGVFFI7266NWTF.csv.gz",
"s3_uri": "s3://igvf-files/2024/12/18/f47c60a6-7a33-42b9-9cb7-a78b17ef7621/IGVFFI7266NWTF.csv.gz",
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/s215194/IGVF/data_submission/reference_files/TF_Perturb_Seq_Pilot_Lenti_CM_PrimaryAnalysis_DE_global.csv.gz",
"upload_status": "invalidated"
},
{
"@id": "/tabular-files/IGVFFI4818IAJW/",
"accession": "IGVFFI4818IAJW",
"aliases": [
"gary-hon:TF_Perturb_Seq_Pilot_Lenti_CM_PrimaryAnalysis_DE_local"
],
"content_type": "unfiltered local differential expression",
"controlled_access": false,
"creation_timestamp": "2024-12-18T19:30:50.456623+00:00",
"file_format": "csv",
"file_size": 6798,
"href": "/tabular-files/IGVFFI4818IAJW/@@download/IGVFFI4818IAJW.csv.gz",
"s3_uri": "s3://igvf-files/2024/12/18/4a810dea-e270-4cff-a8c7-b295f23be862/IGVFFI4818IAJW.csv.gz",
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/s215194/IGVF/data_submission/reference_files/TF_Perturb_Seq_Pilot_Lenti_CM_PrimaryAnalysis_DE_local.csv.gz",
"upload_status": "invalidated"
}
],
"functional_assay_mechanisms": [],
"input_file_sets": [
{
"@id": "/measurement-sets/IGVFDS7834BXBN/",
"accession": "IGVFDS7834BXBN",
"aliases": [
"gary-hon:TF_Perturb_Seq_Pilot_Lenti_CM_LW277"
],
"file_set_type": "experimental data",
"status": "preview"
},
{
"@id": "/auxiliary-sets/IGVFDS8280AMDA/",
"accession": "IGVFDS8280AMDA",
"aliases": [
"gary-hon:TF_Perturb_Seq_Pilot_Lenti_CM_sgRNA_LW277"
],
"file_set_type": "gRNA sequencing",
"status": "preview"
},
{
"@id": "/auxiliary-sets/IGVFDS6231TYIS/",
"accession": "IGVFDS6231TYIS",
"aliases": [
"gary-hon:TF_Perturb_Seq_Pilot_Lenti_CM_HTO_LW277"
],
"file_set_type": "cell hashing barcode sequencing",
"status": "preview"
},
{
"@id": "/measurement-sets/IGVFDS2628PYOH/",
"accession": "IGVFDS2628PYOH",
"aliases": [
"gary-hon:TF_Perturb_Seq_Pilot_Lenti_CM_LW278"
],
"file_set_type": "experimental data",
"status": "preview"
},
{
"@id": "/auxiliary-sets/IGVFDS8139DLEM/",
"accession": "IGVFDS8139DLEM",
"aliases": [
"gary-hon:TF_Perturb_Seq_Pilot_Lenti_CM_sgRNA_LW278"
],
"file_set_type": "gRNA sequencing",
"status": "preview"
},
{
"@id": "/auxiliary-sets/IGVFDS0109SCQO/",
"accession": "IGVFDS0109SCQO",
"aliases": [
"gary-hon:TF_Perturb_Seq_Pilot_Lenti_CM_HTO_LW278"
],
"file_set_type": "cell hashing barcode sequencing",
"status": "preview"
},
{
"@id": "/measurement-sets/IGVFDS7733OTCA/",
"accession": "IGVFDS7733OTCA",
"aliases": [
"gary-hon:TF_Perturb_Seq_Pilot_Lenti_CM_LW279"
],
"file_set_type": "experimental data",
"status": "preview"
},
{
"@id": "/auxiliary-sets/IGVFDS0997MTQA/",
"accession": "IGVFDS0997MTQA",
"aliases": [
"gary-hon:TF_Perturb_Seq_Pilot_Lenti_CM_sgRNA_LW279"
],
"file_set_type": "gRNA sequencing",
"status": "preview"
},
{
"@id": "/auxiliary-sets/IGVFDS7027VRZT/",
"accession": "IGVFDS7027VRZT",
"aliases": [
"gary-hon:TF_Perturb_Seq_Pilot_Lenti_CM_HTO_LW279"
],
"file_set_type": "cell hashing barcode sequencing",
"status": "preview"
},
{
"@id": "/measurement-sets/IGVFDS4852MAUM/",
"accession": "IGVFDS4852MAUM",
"aliases": [
"gary-hon:TF_Perturb_Seq_Pilot_Lenti_CM_LW280"
],
"file_set_type": "experimental data",
"status": "preview"
},
{
"@id": "/auxiliary-sets/IGVFDS6861GRJI/",
"accession": "IGVFDS6861GRJI",
"aliases": [
"gary-hon:TF_Perturb_Seq_Pilot_Lenti_CM_sgRNA_LW280"
],
"file_set_type": "gRNA sequencing",
"status": "preview"
},
{
"@id": "/auxiliary-sets/IGVFDS5228AHGR/",
"accession": "IGVFDS5228AHGR",
"aliases": [
"gary-hon:TF_Perturb_Seq_Pilot_Lenti_CM_HTO_LW280"
],
"file_set_type": "cell hashing barcode sequencing",
"status": "preview"
}
],
"input_for": [],
"lab": {
"@id": "/labs/gary-hon/",
"title": "Gary Hon, UT"
},
"notes": "This object's file_set_type was primary analysis and has been updated to be principal analysis.",
"protocols": [
"https://www.protocols.io/view/experimental-procedures-for-tf-perturb-seq-ut-sout-denf3dbn"
],
"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/IGVFSM7513BJDT/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM7513BJDT",
"aliases": [
"nikhil-munshi:differentited_WTC11_TF_Perturb_Seq_Pilot_CMs_Lenti_LW277"
],
"classifications": [
"differentiated cell specimen"
],
"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) differentiated cell specimen induced to cardiac muscle cell for 12 days (cellular sub pool: subpool_LW277), male, 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/IGVFSM0559UNMK/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM0559UNMK",
"aliases": [
"nikhil-munshi:differentited_WTC11_TF_Perturb_Seq_Pilot_CMs_Lenti_LW279"
],
"classifications": [
"differentiated cell specimen"
],
"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) differentiated cell specimen induced to cardiac muscle cell for 12 days (cellular sub pool: subpool_LW279), male, 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/IGVFSM0604KDJF/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM0604KDJF",
"aliases": [
"nikhil-munshi:differentited_WTC11_TF_Perturb_Seq_Pilot_CMs_Lenti_LW280"
],
"classifications": [
"differentiated cell specimen"
],
"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) differentiated cell specimen induced to cardiac muscle cell for 12 days (cellular sub pool: subpool_LW280), male, 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/IGVFSM7499ZWUW/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM7499ZWUW",
"aliases": [
"nikhil-munshi:differentited_WTC11_TF_Perturb_Seq_Pilot_CMs_Lenti_LW278"
],
"classifications": [
"differentiated cell specimen"
],
"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) differentiated cell specimen induced to cardiac muscle cell for 12 days (cellular sub pool: subpool_LW278), male, 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": "2024-12-17T22:32:29.309598+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": "1a15b925-7d5f-4dcb-87e5-43696e019ff1",
"workflows": [
{
"@id": "/workflows/IGVFWF0190YALU/",
"accession": "IGVFWF0190YALU",
"name": "Hon Perturb-seq Workflow",
"status": "in progress",
"uniform_pipeline": false
}
]
}