{
"@context": "/terms/",
"@id": "/analysis-sets/IGVFDS5498SDRJ/",
"@type": [
"AnalysisSet",
"FileSet",
"Item"
],
"accession": "IGVFDS5498SDRJ",
"aliases": [
"gary-hon:WTC11_CM_Pilot2_Mini_LPv4_PrimaryAnalysis"
],
"assay_titles": [
"Perturb-seq"
],
"audit": {
"ERROR": [
{
"category": "upload status not validated",
"detail": "Tabular file [IGVFFI3722AJJC](/tabular-files/IGVFFI3722AJJC/) has `upload_status` invalidated. Validation error detail: {\"md5sum\": \"original md5sum 64916d57065e7d1c441e0fc4feb11a0d does not match newly calculated md5sum a7c389215a18d4b836f0376a1931d96a.\"}. Files are expected to be validated or validation exempted.",
"level": 60,
"level_name": "ERROR",
"name": "audit_upload_status",
"path": "/tabular-files/IGVFFI3722AJJC/"
},
{
"category": "upload status not validated",
"detail": "Tabular file [IGVFFI0141RZRZ](/tabular-files/IGVFFI0141RZRZ/) has `upload_status` invalidated. Validation error detail: {\"md5sum\": \"original md5sum 94a0a68e08da62551d35d2d786bf1f01 does not match newly calculated md5sum 8de646fb0adeb46f99f73f15baa9816a.\"}. Files are expected to be validated or validation exempted.",
"level": 60,
"level_name": "ERROR",
"name": "audit_upload_status",
"path": "/tabular-files/IGVFFI0141RZRZ/"
},
{
"category": "unexpected input file set",
"detail": "Analysis set [IGVFDS5498SDRJ](/analysis-sets/IGVFDS5498SDRJ/) links to file set(s): [IGVFDS3215JVHK](/auxiliary-sets/IGVFDS3215JVHK/), [IGVFDS0373CFJS](/auxiliary-sets/IGVFDS0373CFJS/), [IGVFDS5699EGGK](/auxiliary-sets/IGVFDS5699EGGK/), [IGVFDS3695BOGD](/measurement-sets/IGVFDS3695BOGD/), [IGVFDS4629NPBV](/measurement-sets/IGVFDS4629NPBV/), [IGVFDS2536BETY](/auxiliary-sets/IGVFDS2536BETY/), [IGVFDS6863PGGX](/measurement-sets/IGVFDS6863PGGX/), [IGVFDS4935NKQB](/auxiliary-sets/IGVFDS4935NKQB/), [IGVFDS4210TUPX](/auxiliary-sets/IGVFDS4210TUPX/), [IGVFDS2827ZGPM](/measurement-sets/IGVFDS2827ZGPM/), [IGVFDS3364ARLO](/auxiliary-sets/IGVFDS3364ARLO/), [IGVFDS0465GFSG](/auxiliary-sets/IGVFDS0465GFSG/) 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/IGVFDS5498SDRJ/"
}
],
"INTERNAL_ACTION": [
{
"category": "mismatched status",
"detail": "Preview matrix file [IGVFFI5439VMRC](/matrix-files/IGVFFI5439VMRC/) 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/IGVFFI5439VMRC/"
},
{
"category": "mismatched status",
"detail": "Preview matrix file [IGVFFI1746RIFK](/matrix-files/IGVFFI1746RIFK/) 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/IGVFFI1746RIFK/"
},
{
"category": "mismatched status",
"detail": "Preview matrix file [IGVFFI7502QSNY](/matrix-files/IGVFFI7502QSNY/) 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/IGVFFI7502QSNY/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing file format specifications",
"detail": "Tabular file [IGVFFI3722AJJC](/tabular-files/IGVFFI3722AJJC/) 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/IGVFFI3722AJJC/"
},
{
"category": "missing file format specifications",
"detail": "Tabular file [IGVFFI0141RZRZ](/tabular-files/IGVFFI0141RZRZ/) 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/IGVFFI0141RZRZ/"
},
{
"category": "missing analysis step version",
"detail": "Analysis set [IGVFDS5498SDRJ](/analysis-sets/IGVFDS5498SDRJ/) links to file(s) [IGVFFI3722AJJC](/tabular-files/IGVFFI3722AJJC/), [IGVFFI0141RZRZ](/tabular-files/IGVFFI0141RZRZ/) 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/IGVFDS5498SDRJ/"
},
{
"category": "missing derived from",
"detail": "Analysis set [IGVFDS5498SDRJ](/analysis-sets/IGVFDS5498SDRJ/) links to file(s) [IGVFFI7502QSNY](/matrix-files/IGVFFI7502QSNY/), [IGVFFI5439VMRC](/matrix-files/IGVFFI5439VMRC/), [IGVFFI1746RIFK](/matrix-files/IGVFFI1746RIFK/), [IGVFFI3722AJJC](/tabular-files/IGVFFI3722AJJC/), [IGVFFI0141RZRZ](/tabular-files/IGVFFI0141RZRZ/) 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/IGVFDS5498SDRJ/"
}
]
},
"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": "2024-12-04T20:07:32.444041+00:00",
"donors": [
{
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"accession": "IGVFDO1756PPKO",
"aliases": [
"igvf:donor_of_WTC11"
],
"sex": "male",
"status": "released",
"taxa": "Homo sapiens"
}
],
"file_set_type": "principal analysis",
"files": [
{
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"accession": "IGVFFI7502QSNY",
"aliases": [
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],
"content_type": "sparse gene count matrix",
"creation_timestamp": "2024-12-17T22:46:12.388714+00:00",
"file_format": "h5ad",
"file_size": 8633573630,
"href": "/matrix-files/IGVFFI7502QSNY/@@download/IGVFFI7502QSNY.h5ad",
"s3_uri": "s3://igvf-files/2024/12/17/2c8c0c2b-b9dc-4477-9749-0a76cc51ed09/IGVFFI7502QSNY.h5ad",
"status": "preview",
"submitted_file_name": "/project/shared/gcrb_igvf/data/shared/mini_cm_pilot02_LPv4/H5AD/V0._mini_cm02_LPv4_sgRNACells_filtered_w_embedding.h5ad",
"upload_status": "validated"
},
{
"@id": "/matrix-files/IGVFFI5439VMRC/",
"accession": "IGVFFI5439VMRC",
"aliases": [
"gary-hon:WTC11_CM_Pilot2_Mini_LPv4_PrimaryAnalysis_h5"
],
"content_type": "filtered feature barcode matrix",
"creation_timestamp": "2024-12-17T23:42:37.689714+00:00",
"file_format": "hdf5",
"file_size": 767591830,
"href": "/matrix-files/IGVFFI5439VMRC/@@download/IGVFFI5439VMRC.h5",
"s3_uri": "s3://igvf-files/2024/12/17/c6c23dfa-2e3d-4e90-8698-a33af425b1ef/IGVFFI5439VMRC.h5",
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/s215194/Single_Cell/mini_cm_pilot_02_inducible/_427-430_Lpv4/_aggr_transcriptome/cm_pilot_mini_02_no_normalization_LPv4/outs/count/filtered_feature_bc_matrix.h5",
"upload_status": "validated"
},
{
"@id": "/matrix-files/IGVFFI1746RIFK/",
"accession": "IGVFFI1746RIFK",
"aliases": [
"gary-hon:WTC11_CM_Pilot2_Mini_LPv4_PrimaryAnalysis_pkl"
],
"content_type": "raw feature barcode matrix",
"creation_timestamp": "2024-12-17T23:42:57.250424+00:00",
"file_format": "pkl",
"file_size": 1029340657,
"href": "/matrix-files/IGVFFI1746RIFK/@@download/IGVFFI1746RIFKpkl",
"s3_uri": "s3://igvf-files/2024/12/17/17499843-d28b-408c-8b83-fb0b90deacd6/IGVFFI1746RIFKpkl",
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/s215194/Single_Cell/mini_cm_pilot_02_inducible/_427-430_Lpv4/aggr_dataframe/aggr_combined_df_full.pkl",
"upload_status": "validated"
},
{
"@id": "/tabular-files/IGVFFI3722AJJC/",
"accession": "IGVFFI3722AJJC",
"aliases": [
"gary-hon:WTC11_CM_Pilot2_Mini_LPv4_PrimaryAnalysis_DE_local"
],
"content_type": "unfiltered local differential expression",
"controlled_access": false,
"creation_timestamp": "2024-12-18T20:47:40.135033+00:00",
"file_format": "csv",
"file_size": 2876,
"href": "/tabular-files/IGVFFI3722AJJC/@@download/IGVFFI3722AJJC.csv.gz",
"s3_uri": "s3://igvf-files/2024/12/18/3de45f19-6f02-487c-a2c7-9b24638a93d8/IGVFFI3722AJJC.csv.gz",
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/s215194/IGVF/data_submission/reference_files/WTC11_CM_Pilot2_Mini_LPv4_PrimaryAnalysis_DE_local.csv.gz",
"upload_status": "invalidated"
},
{
"@id": "/tabular-files/IGVFFI0141RZRZ/",
"accession": "IGVFFI0141RZRZ",
"aliases": [
"gary-hon:WTC11_CM_Pilot2_Mini_LPv4_PrimaryAnalysis_DE_global"
],
"content_type": "unfiltered global differential expression",
"controlled_access": false,
"creation_timestamp": "2024-12-18T20:47:52.299360+00:00",
"file_format": "csv",
"file_size": 32646,
"href": "/tabular-files/IGVFFI0141RZRZ/@@download/IGVFFI0141RZRZ.csv.gz",
"s3_uri": "s3://igvf-files/2024/12/18/8e91f719-30a4-48ed-b731-2d863315241d/IGVFFI0141RZRZ.csv.gz",
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/s215194/IGVF/data_submission/reference_files/WTC11_CM_Pilot2_Mini_LPv4_PrimaryAnalysis_DE_global.csv.gz",
"upload_status": "invalidated"
}
],
"functional_assay_mechanisms": [],
"input_file_sets": [
{
"@id": "/measurement-sets/IGVFDS6863PGGX/",
"accession": "IGVFDS6863PGGX",
"aliases": [
"gary-hon:differentited_WTC11_CM_Pilot2_Mini_LPv4_LW427"
],
"file_set_type": "experimental data",
"status": "preview"
},
{
"@id": "/auxiliary-sets/IGVFDS0465GFSG/",
"accession": "IGVFDS0465GFSG",
"aliases": [
"gary-hon:differentited_WTC11_CM_Pilot2_Mini_LPv4_sgRNA_LW427"
],
"file_set_type": "gRNA sequencing",
"status": "preview"
},
{
"@id": "/auxiliary-sets/IGVFDS5699EGGK/",
"accession": "IGVFDS5699EGGK",
"aliases": [
"gary-hon:differentited_WTC11_CM_Pilot2_Mini_LPv4_HTO_LW427"
],
"file_set_type": "cell hashing barcode sequencing",
"status": "preview"
},
{
"@id": "/measurement-sets/IGVFDS4629NPBV/",
"accession": "IGVFDS4629NPBV",
"aliases": [
"gary-hon:differentited_WTC11_CM_Pilot2_Mini_LPv4_LW428"
],
"file_set_type": "experimental data",
"status": "preview"
},
{
"@id": "/auxiliary-sets/IGVFDS2536BETY/",
"accession": "IGVFDS2536BETY",
"aliases": [
"gary-hon:differentited_WTC11_CM_Pilot2_Mini_LPv4_sgRNA_LW428"
],
"file_set_type": "gRNA sequencing",
"status": "preview"
},
{
"@id": "/auxiliary-sets/IGVFDS3364ARLO/",
"accession": "IGVFDS3364ARLO",
"aliases": [
"gary-hon:differentited_WTC11_CM_Pilot2_Mini_LPv4_HTO_LW428"
],
"file_set_type": "cell hashing barcode sequencing",
"status": "preview"
},
{
"@id": "/measurement-sets/IGVFDS3695BOGD/",
"accession": "IGVFDS3695BOGD",
"aliases": [
"gary-hon:differentited_WTC11_CM_Pilot2_Mini_LPv4_LW429"
],
"file_set_type": "experimental data",
"status": "preview"
},
{
"@id": "/auxiliary-sets/IGVFDS4935NKQB/",
"accession": "IGVFDS4935NKQB",
"aliases": [
"gary-hon:differentited_WTC11_CM_Pilot2_Mini_LPv4_sgRNA_LW429"
],
"file_set_type": "gRNA sequencing",
"status": "preview"
},
{
"@id": "/auxiliary-sets/IGVFDS4210TUPX/",
"accession": "IGVFDS4210TUPX",
"aliases": [
"gary-hon:differentited_WTC11_CM_Pilot2_Mini_LPv4_HTO_LW429"
],
"file_set_type": "cell hashing barcode sequencing",
"status": "preview"
},
{
"@id": "/measurement-sets/IGVFDS2827ZGPM/",
"accession": "IGVFDS2827ZGPM",
"aliases": [
"gary-hon:differentited_WTC11_CM_Pilot2_Mini_LPv4_LW430"
],
"file_set_type": "experimental data",
"status": "preview"
},
{
"@id": "/auxiliary-sets/IGVFDS0373CFJS/",
"accession": "IGVFDS0373CFJS",
"aliases": [
"gary-hon:differentited_WTC11_CM_Pilot2_Mini_PB9_sgRNA_LW438"
],
"file_set_type": "gRNA sequencing",
"status": "preview"
},
{
"@id": "/auxiliary-sets/IGVFDS3215JVHK/",
"accession": "IGVFDS3215JVHK",
"aliases": [
"gary-hon:differentited_WTC11_CM_Pilot2_Mini_LPv4_HTO_LW430"
],
"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) 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/IGVFSM7766HOYF/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM7766HOYF",
"aliases": [
"nikhil-munshi:differentited_WTC11_CM_Pilot2_Mini_LPv4_LW429"
],
"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_LW429), 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/IGVFSM0565MLZG/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM0565MLZG",
"aliases": [
"nikhil-munshi:differentited_WTC11_CM_Pilot2_Mini_LPv4_LW427"
],
"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_LW427), 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/IGVFSM2127MVQH/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM2127MVQH",
"aliases": [
"nikhil-munshi:differentited_WTC11_CM_Pilot2_Mini_LPv4_LW430"
],
"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_LW430), 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/IGVFSM9285BBSI/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM9285BBSI",
"aliases": [
"nikhil-munshi:differentited_WTC11_CM_Pilot2_Mini_LPv4_LW428"
],
"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_LW428), 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/IGVFSM2176YXFG/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM2176YXFG",
"aliases": [
"nikhil-munshi:differentited_WTC11_CM_Pilot2_Mini_PB9_LW438"
],
"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_LW438), 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": "2024-12-17T22:46:12.388714+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": "b66e7cc5-5410-4e77-9437-f9df054bc0c0",
"workflows": [
{
"@id": "/workflows/IGVFWF0190YALU/",
"accession": "IGVFWF0190YALU",
"name": "Hon Perturb-seq Workflow",
"status": "in progress",
"uniform_pipeline": false
}
]
}