{
"@context": "/terms/",
"@id": "/analysis-sets/IGVFDS4003HZAB/",
"@type": [
"AnalysisSet",
"FileSet",
"Item"
],
"accession": "IGVFDS4003HZAB",
"aliases": [
"gary-hon:CM_Pilot_2_Lenti_RNA"
],
"assay_titles": [
"Perturb-seq"
],
"audit": {
"ERROR": [
{
"category": "upload status not validated",
"detail": "Tabular file [IGVFFI6770EFUQ](/tabular-files/IGVFFI6770EFUQ/) has `upload_status` invalidated. Validation error detail: {\"md5sum\": \"original md5sum d954cfa2410643223f1e2a6e2335943e does not match newly calculated md5sum 9f8c758279c6887f72762b8b48f814fe.\"}. Files are expected to be validated or validation exempted.",
"level": 60,
"level_name": "ERROR",
"name": "audit_upload_status",
"path": "/tabular-files/IGVFFI6770EFUQ/"
},
{
"category": "unexpected input file set",
"detail": "Analysis set [IGVFDS4003HZAB](/analysis-sets/IGVFDS4003HZAB/) links to file set(s): [IGVFDS3533NRTW](/auxiliary-sets/IGVFDS3533NRTW/), [IGVFDS5931MYJN](/measurement-sets/IGVFDS5931MYJN/), [IGVFDS3633OXMI](/auxiliary-sets/IGVFDS3633OXMI/), [IGVFDS8001EMIV](/auxiliary-sets/IGVFDS8001EMIV/), [IGVFDS6297HIRK](/auxiliary-sets/IGVFDS6297HIRK/), [IGVFDS7783CMAZ](/auxiliary-sets/IGVFDS7783CMAZ/), [IGVFDS0262BREE](/measurement-sets/IGVFDS0262BREE/), [IGVFDS4088YJYC](/measurement-sets/IGVFDS4088YJYC/), [IGVFDS4926IAGY](/auxiliary-sets/IGVFDS4926IAGY/), [IGVFDS6787YPNQ](/auxiliary-sets/IGVFDS6787YPNQ/), [IGVFDS5173WYKU](/measurement-sets/IGVFDS5173WYKU/), [IGVFDS6054GEKL](/measurement-sets/IGVFDS6054GEKL/), [IGVFDS0347EJHA](/auxiliary-sets/IGVFDS0347EJHA/), [IGVFDS1349DIMY](/auxiliary-sets/IGVFDS1349DIMY/), [IGVFDS8445PWTI](/auxiliary-sets/IGVFDS8445PWTI/), [IGVFDS9572XHUR](/measurement-sets/IGVFDS9572XHUR/), [IGVFDS3499IMSW](/auxiliary-sets/IGVFDS3499IMSW/), [IGVFDS4965SLDK](/measurement-sets/IGVFDS4965SLDK/), [IGVFDS7126MOZN](/auxiliary-sets/IGVFDS7126MOZN/), [IGVFDS1373ALPP](/auxiliary-sets/IGVFDS1373ALPP/), [IGVFDS5033OBAO](/measurement-sets/IGVFDS5033OBAO/), [IGVFDS3625MSZP](/auxiliary-sets/IGVFDS3625MSZP/), [IGVFDS7944GWTS](/auxiliary-sets/IGVFDS7944GWTS/), [IGVFDS5031XGGB](/auxiliary-sets/IGVFDS5031XGGB/) 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/IGVFDS4003HZAB/"
},
{
"category": "upload status not validated",
"detail": "Tabular file [IGVFFI2164BNCK](/tabular-files/IGVFFI2164BNCK/) has `upload_status` invalidated. Validation error detail: {\"md5sum\": \"original md5sum dfbfbd18022497f36ae6313fa67fc814 does not match newly calculated md5sum ba4b511ed4495f6e6064a6fa7fcd7e58.\"}. Files are expected to be validated or validation exempted.",
"level": 60,
"level_name": "ERROR",
"name": "audit_upload_status",
"path": "/tabular-files/IGVFFI2164BNCK/"
}
],
"INTERNAL_ACTION": [
{
"category": "mismatched status",
"detail": "Preview matrix file [IGVFFI0468AHGV](/matrix-files/IGVFFI0468AHGV/) 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/IGVFFI0468AHGV/"
},
{
"category": "mismatched status",
"detail": "Preview matrix file [IGVFFI6973SBDI](/matrix-files/IGVFFI6973SBDI/) 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/IGVFFI6973SBDI/"
},
{
"category": "mismatched status",
"detail": "Preview matrix file [IGVFFI7916RANR](/matrix-files/IGVFFI7916RANR/) 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/IGVFFI7916RANR/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing file format specifications",
"detail": "Tabular file [IGVFFI6770EFUQ](/tabular-files/IGVFFI6770EFUQ/) 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/IGVFFI6770EFUQ/"
},
{
"category": "missing analysis step version",
"detail": "Analysis set [IGVFDS4003HZAB](/analysis-sets/IGVFDS4003HZAB/) links to file(s) [IGVFFI2164BNCK](/tabular-files/IGVFFI2164BNCK/), [IGVFFI6770EFUQ](/tabular-files/IGVFFI6770EFUQ/) 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/IGVFDS4003HZAB/"
},
{
"category": "missing derived from",
"detail": "Analysis set [IGVFDS4003HZAB](/analysis-sets/IGVFDS4003HZAB/) links to file(s) [IGVFFI7916RANR](/matrix-files/IGVFFI7916RANR/), [IGVFFI6973SBDI](/matrix-files/IGVFFI6973SBDI/), [IGVFFI0468AHGV](/matrix-files/IGVFFI0468AHGV/), [IGVFFI2164BNCK](/tabular-files/IGVFFI2164BNCK/), [IGVFFI6770EFUQ](/tabular-files/IGVFFI6770EFUQ/) 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/IGVFDS4003HZAB/"
},
{
"category": "missing file format specifications",
"detail": "Tabular file [IGVFFI2164BNCK](/tabular-files/IGVFFI2164BNCK/) 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/IGVFFI2164BNCK/"
}
]
},
"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": "2024-12-04T22:34:28.118783+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/IGVFFI7916RANR/",
"accession": "IGVFFI7916RANR",
"aliases": [
"gary-hon:CM_Pilot_2_Lenti_RNA_h5ad"
],
"content_type": "sparse gene count matrix",
"creation_timestamp": "2024-12-17T22:56:19.790450+00:00",
"file_format": "h5ad",
"file_size": 20565294501,
"href": "/matrix-files/IGVFFI7916RANR/@@download/IGVFFI7916RANR.h5ad",
"s3_uri": "s3://igvf-files/2024/12/17/89bbc5ca-abb1-40b9-9f69-a1badb4afe0a/IGVFFI7916RANR.h5ad",
"status": "preview",
"submitted_file_name": "/project/shared/gcrb_igvf/data/shared/CMPILOT2_scRNAseq/H5AD/V0_CM_Pilot#02_Lenti_reprocessed_sgRNACells_filtered_w_embedding_full.h5ad",
"upload_status": "validated"
},
{
"@id": "/matrix-files/IGVFFI6973SBDI/",
"accession": "IGVFFI6973SBDI",
"aliases": [
"gary-hon:CM_Pilot_2_Lenti_RNA_h5"
],
"content_type": "filtered feature barcode matrix",
"creation_timestamp": "2024-12-17T23:46:30.308297+00:00",
"file_format": "hdf5",
"file_size": 443421981,
"href": "/matrix-files/IGVFFI6973SBDI/@@download/IGVFFI6973SBDI.h5",
"s3_uri": "s3://igvf-files/2024/12/17/dba2c5ff-793d-499d-ae31-0059d5719b5c/IGVFFI6973SBDI.h5",
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/s215194/Single_Cell/Process_scRNA_CMPILOT2_Lenti/_pipeline_reprocessing/_all_lanes_combined/aggr_transcriptome/CMPILOT2_Lenti_MN/outs/count/filtered_feature_bc_matrix.h5",
"upload_status": "validated"
},
{
"@id": "/matrix-files/IGVFFI0468AHGV/",
"accession": "IGVFFI0468AHGV",
"aliases": [
"gary-hon:CM_Pilot_2_Lenti_RNA_pkl"
],
"content_type": "raw feature barcode matrix",
"creation_timestamp": "2024-12-17T23:46:51.301513+00:00",
"file_format": "pkl",
"file_size": 5175687361,
"href": "/matrix-files/IGVFFI0468AHGV/@@download/IGVFFI0468AHGVpkl",
"s3_uri": "s3://igvf-files/2024/12/17/f17ae54a-c1e4-4200-8d60-e95bfb47c3ef/IGVFFI0468AHGVpkl",
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/s215194/Single_Cell/Process_scRNA_CMPILOT2_Lenti/_pipeline_reprocessing/_all_lanes_combined/aggr_dataframe/aggr_combined_df_full.pkl",
"upload_status": "validated"
},
{
"@id": "/tabular-files/IGVFFI2164BNCK/",
"accession": "IGVFFI2164BNCK",
"aliases": [
"gary-hon:CM_Pilot_2_Lenti_RNA_DE_local"
],
"content_type": "unfiltered local differential expression",
"controlled_access": false,
"creation_timestamp": "2024-12-18T20:49:01.976231+00:00",
"file_format": "csv",
"file_size": 5721,
"href": "/tabular-files/IGVFFI2164BNCK/@@download/IGVFFI2164BNCK.csv.gz",
"s3_uri": "s3://igvf-files/2024/12/18/001538f5-2833-4afb-862b-86747d1cafcc/IGVFFI2164BNCK.csv.gz",
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/s215194/IGVF/data_submission/reference_files/CM_Pilot_2_Lenti_RNA_DE_local.csv.gz",
"upload_status": "invalidated"
},
{
"@id": "/tabular-files/IGVFFI6770EFUQ/",
"accession": "IGVFFI6770EFUQ",
"aliases": [
"gary-hon:CM_Pilot_2_Lenti_RNA_DE_global"
],
"content_type": "unfiltered global differential expression",
"controlled_access": false,
"creation_timestamp": "2024-12-18T20:49:22.567666+00:00",
"file_format": "csv",
"file_size": 272820,
"href": "/tabular-files/IGVFFI6770EFUQ/@@download/IGVFFI6770EFUQ.csv.gz",
"s3_uri": "s3://igvf-files/2024/12/18/1701c914-2362-44fe-9a68-4b4edc698472/IGVFFI6770EFUQ.csv.gz",
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/s215194/IGVF/data_submission/reference_files/CM_Pilot_2_Lenti_RNA_DE_global.csv.gz",
"upload_status": "invalidated"
}
],
"functional_assay_mechanisms": [],
"input_file_sets": [
{
"@id": "/measurement-sets/IGVFDS0262BREE/",
"accession": "IGVFDS0262BREE",
"aliases": [
"gary-hon:CM_Pilot_2_Lenti_RNA_LW261"
],
"file_set_type": "experimental data",
"status": "preview"
},
{
"@id": "/auxiliary-sets/IGVFDS7783CMAZ/",
"accession": "IGVFDS7783CMAZ",
"aliases": [
"gary-hon:CM_Pilot_2_Lenti_HTO_LW261"
],
"file_set_type": "cell hashing barcode sequencing",
"status": "preview"
},
{
"@id": "/auxiliary-sets/IGVFDS1373ALPP/",
"accession": "IGVFDS1373ALPP",
"aliases": [
"gary-hon:CM_Pilot_2_Lenti_sgRNA_LW261"
],
"file_set_type": "gRNA sequencing",
"status": "preview"
},
{
"@id": "/measurement-sets/IGVFDS9572XHUR/",
"accession": "IGVFDS9572XHUR",
"aliases": [
"gary-hon:CM_Pilot_2_Lenti_RNA_LW262"
],
"file_set_type": "experimental data",
"status": "preview"
},
{
"@id": "/auxiliary-sets/IGVFDS6297HIRK/",
"accession": "IGVFDS6297HIRK",
"aliases": [
"gary-hon:CM_Pilot_2_Lenti_HTO_LW262"
],
"file_set_type": "cell hashing barcode sequencing",
"status": "preview"
},
{
"@id": "/auxiliary-sets/IGVFDS0347EJHA/",
"accession": "IGVFDS0347EJHA",
"aliases": [
"gary-hon:CM_Pilot_2_Lenti_sgRNA_LW262"
],
"file_set_type": "gRNA sequencing",
"status": "preview"
},
{
"@id": "/measurement-sets/IGVFDS4965SLDK/",
"accession": "IGVFDS4965SLDK",
"aliases": [
"gary-hon:CM_Pilot_2_Lenti_RNA_LW263"
],
"file_set_type": "experimental data",
"status": "preview"
},
{
"@id": "/auxiliary-sets/IGVFDS3499IMSW/",
"accession": "IGVFDS3499IMSW",
"aliases": [
"gary-hon:CM_Pilot_2_Lenti_HTO_LW263"
],
"file_set_type": "cell hashing barcode sequencing",
"status": "preview"
},
{
"@id": "/auxiliary-sets/IGVFDS1349DIMY/",
"accession": "IGVFDS1349DIMY",
"aliases": [
"gary-hon:CM_Pilot_2_Lenti_sgRNA_LW263"
],
"file_set_type": "gRNA sequencing",
"status": "preview"
},
{
"@id": "/measurement-sets/IGVFDS6054GEKL/",
"accession": "IGVFDS6054GEKL",
"aliases": [
"gary-hon:CM_Pilot_2_Lenti_RNA_LW264"
],
"file_set_type": "experimental data",
"status": "preview"
},
{
"@id": "/auxiliary-sets/IGVFDS4926IAGY/",
"accession": "IGVFDS4926IAGY",
"aliases": [
"gary-hon:CM_Pilot_2_Lenti_HTO_LW264"
],
"file_set_type": "cell hashing barcode sequencing",
"status": "preview"
},
{
"@id": "/auxiliary-sets/IGVFDS3533NRTW/",
"accession": "IGVFDS3533NRTW",
"aliases": [
"gary-hon:CM_Pilot_2_Lenti_sgRNA_LW264"
],
"file_set_type": "gRNA sequencing",
"status": "preview"
},
{
"@id": "/measurement-sets/IGVFDS5033OBAO/",
"accession": "IGVFDS5033OBAO",
"aliases": [
"gary-hon:CM_Pilot_2_Lenti_RNA_LW265"
],
"file_set_type": "experimental data",
"status": "preview"
},
{
"@id": "/auxiliary-sets/IGVFDS3633OXMI/",
"accession": "IGVFDS3633OXMI",
"aliases": [
"gary-hon:CM_Pilot_2_Lenti_HTO_LW265"
],
"file_set_type": "cell hashing barcode sequencing",
"status": "preview"
},
{
"@id": "/auxiliary-sets/IGVFDS7126MOZN/",
"accession": "IGVFDS7126MOZN",
"aliases": [
"gary-hon:CM_Pilot_2_Lenti_sgRNA_LW265"
],
"file_set_type": "gRNA sequencing",
"status": "preview"
},
{
"@id": "/measurement-sets/IGVFDS5931MYJN/",
"accession": "IGVFDS5931MYJN",
"aliases": [
"gary-hon:CM_Pilot_2_Lenti_RNA_LW266"
],
"file_set_type": "experimental data",
"status": "preview"
},
{
"@id": "/auxiliary-sets/IGVFDS8001EMIV/",
"accession": "IGVFDS8001EMIV",
"aliases": [
"gary-hon:CM_Pilot_2_Lenti_HTO_LW266"
],
"file_set_type": "cell hashing barcode sequencing",
"status": "preview"
},
{
"@id": "/auxiliary-sets/IGVFDS7944GWTS/",
"accession": "IGVFDS7944GWTS",
"aliases": [
"gary-hon:CM_Pilot_2_Lenti_sgRNA_LW266"
],
"file_set_type": "gRNA sequencing",
"status": "preview"
},
{
"@id": "/measurement-sets/IGVFDS4088YJYC/",
"accession": "IGVFDS4088YJYC",
"aliases": [
"gary-hon:CM_Pilot_2_Lenti_RNA_LW267"
],
"file_set_type": "experimental data",
"status": "preview"
},
{
"@id": "/auxiliary-sets/IGVFDS8445PWTI/",
"accession": "IGVFDS8445PWTI",
"aliases": [
"gary-hon:CM_Pilot_2_Lenti_HTO_LW267"
],
"file_set_type": "cell hashing barcode sequencing",
"status": "preview"
},
{
"@id": "/auxiliary-sets/IGVFDS6787YPNQ/",
"accession": "IGVFDS6787YPNQ",
"aliases": [
"gary-hon:CM_Pilot_2_Lenti_sgRNA_LW267"
],
"file_set_type": "gRNA sequencing",
"status": "preview"
},
{
"@id": "/measurement-sets/IGVFDS5173WYKU/",
"accession": "IGVFDS5173WYKU",
"aliases": [
"gary-hon:CM_Pilot_2_Lenti_RNA_LW268"
],
"file_set_type": "experimental data",
"status": "preview"
},
{
"@id": "/auxiliary-sets/IGVFDS3625MSZP/",
"accession": "IGVFDS3625MSZP",
"aliases": [
"gary-hon:CM_Pilot_2_Lenti_HTO_LW268"
],
"file_set_type": "cell hashing barcode sequencing",
"status": "preview"
},
{
"@id": "/auxiliary-sets/IGVFDS5031XGGB/",
"accession": "IGVFDS5031XGGB",
"aliases": [
"gary-hon:CM_Pilot_2_Lenti_sgRNA_LW268"
],
"file_set_type": "gRNA 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/IGVFSM0248SELV/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM0248SELV",
"aliases": [
"nikhil-munshi:differentited_WTC11_CM_Pilot1_Lenti_LW262"
],
"classifications": [
"differentiated cell specimen"
],
"construct_library_sets": [
"/construct-library-sets/IGVFDS9629YZLO/"
],
"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_LW262), 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/IGVFSM7215JDPM/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM7215JDPM",
"aliases": [
"nikhil-munshi:differentited_WTC11_CM_Pilot1_Lenti_LW265"
],
"classifications": [
"differentiated cell specimen"
],
"construct_library_sets": [
"/construct-library-sets/IGVFDS9629YZLO/"
],
"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_LW265), 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/IGVFSM4930FDUF/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM4930FDUF",
"aliases": [
"nikhil-munshi:differentited_WTC11_CM_Pilot1_Lenti_LW266"
],
"classifications": [
"differentiated cell specimen"
],
"construct_library_sets": [
"/construct-library-sets/IGVFDS9629YZLO/"
],
"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_LW266), 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/IGVFSM5628VVVG/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM5628VVVG",
"aliases": [
"nikhil-munshi:differentited_WTC11_CM_Pilot1_Lenti_LW267"
],
"classifications": [
"differentiated cell specimen"
],
"construct_library_sets": [
"/construct-library-sets/IGVFDS9629YZLO/"
],
"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_LW267), 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/IGVFSM2215YBLM/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM2215YBLM",
"aliases": [
"nikhil-munshi:differentited_WTC11_CM_Pilot1_Lenti_LW268"
],
"classifications": [
"differentiated cell specimen"
],
"construct_library_sets": [
"/construct-library-sets/IGVFDS9629YZLO/"
],
"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_LW268), 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/IGVFSM0981UTUA/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM0981UTUA",
"aliases": [
"nikhil-munshi:differentited_WTC11_CM_Pilot1_Lenti_LW264"
],
"classifications": [
"differentiated cell specimen"
],
"construct_library_sets": [
"/construct-library-sets/IGVFDS9629YZLO/"
],
"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_LW264), 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/IGVFSM1972EKCJ/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM1972EKCJ",
"aliases": [
"nikhil-munshi:differentited_WTC11_CM_Pilot1_Lenti_LW261"
],
"classifications": [
"differentiated cell specimen"
],
"construct_library_sets": [
"/construct-library-sets/IGVFDS9629YZLO/"
],
"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_LW261), 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/IGVFSM0333RWYR/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM0333RWYR",
"aliases": [
"nikhil-munshi:differentited_WTC11_CM_Pilot1_Lenti_LW263"
],
"classifications": [
"differentiated cell specimen"
],
"construct_library_sets": [
"/construct-library-sets/IGVFDS9629YZLO/"
],
"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_LW263), 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": "2024-12-17T22:56:19.790450+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": "d8e1c827-68b5-4899-9be1-2012403dbd86",
"workflows": [
{
"@id": "/workflows/IGVFWF0190YALU/",
"accession": "IGVFWF0190YALU",
"name": "Hon Perturb-seq Workflow",
"status": "in progress",
"uniform_pipeline": false
}
]
}