{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS3701EFIG/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS3701EFIG",
"aliases": [
"gary-hon:differentited_WTC11_CM_Pilot2_Mini_PB9_HTO_LW438"
],
"audit": {
"ERROR": [
{
"category": "inconsistent sequencing kit",
"detail": "Auxiliary set [IGVFDS3701EFIG](/auxiliary-sets/IGVFDS3701EFIG/) has a sequence file [IGVFFI2410SQSR](/sequence-files/IGVFFI2410SQSR/) sequenced on a `sequencing_platform` [EFO_0008637](/platform-terms/EFO_0008637/) that is inconsistent with its `sequencing_kit` NovaSeq X Series 25B Reagent Kit. Sequence files should specify a sequencing kit which is consistent with their sequencing platform. Sequence files in the same sequencing run should also specify the same sequencing kit.",
"level": 60,
"level_name": "ERROR",
"name": "audit_inconsistent_sequencing_kit",
"path": "/auxiliary-sets/IGVFDS3701EFIG/"
},
{
"category": "inconsistent sequencing kit",
"detail": "Auxiliary set [IGVFDS3701EFIG](/auxiliary-sets/IGVFDS3701EFIG/) has a sequence file [IGVFFI9959PZPC](/sequence-files/IGVFFI9959PZPC/) sequenced on a `sequencing_platform` [EFO_0008637](/platform-terms/EFO_0008637/) that is inconsistent with its `sequencing_kit` NovaSeq X Series 25B Reagent Kit. Sequence files should specify a sequencing kit which is consistent with their sequencing platform. Sequence files in the same sequencing run should also specify the same sequencing kit.",
"level": 60,
"level_name": "ERROR",
"name": "audit_inconsistent_sequencing_kit",
"path": "/auxiliary-sets/IGVFDS3701EFIG/"
},
{
"category": "inconsistent sequencing kit",
"detail": "Auxiliary set [IGVFDS3701EFIG](/auxiliary-sets/IGVFDS3701EFIG/) has a sequence file [IGVFFI9583JOVR](/sequence-files/IGVFFI9583JOVR/) sequenced on a `sequencing_platform` [EFO_0008637](/platform-terms/EFO_0008637/) that is inconsistent with its `sequencing_kit` NovaSeq X Series 25B Reagent Kit. Sequence files should specify a sequencing kit which is consistent with their sequencing platform. Sequence files in the same sequencing run should also specify the same sequencing kit.",
"level": 60,
"level_name": "ERROR",
"name": "audit_inconsistent_sequencing_kit",
"path": "/auxiliary-sets/IGVFDS3701EFIG/"
},
{
"category": "inconsistent sequencing kit",
"detail": "Auxiliary set [IGVFDS3701EFIG](/auxiliary-sets/IGVFDS3701EFIG/) has a sequence file [IGVFFI0287KKJM](/sequence-files/IGVFFI0287KKJM/) sequenced on a `sequencing_platform` [EFO_0008637](/platform-terms/EFO_0008637/) that is inconsistent with its `sequencing_kit` NovaSeq X Series 25B Reagent Kit. Sequence files should specify a sequencing kit which is consistent with their sequencing platform. Sequence files in the same sequencing run should also specify the same sequencing kit.",
"level": 60,
"level_name": "ERROR",
"name": "audit_inconsistent_sequencing_kit",
"path": "/auxiliary-sets/IGVFDS3701EFIG/"
}
],
"INTERNAL_ACTION": [
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS3701EFIG](/auxiliary-sets/IGVFDS3701EFIG/) has sequence file(s): [IGVFFI2410SQSR](/sequence-files/IGVFFI2410SQSR/), [IGVFFI9959PZPC](/sequence-files/IGVFFI9959PZPC/), [IGVFFI9583JOVR](/sequence-files/IGVFFI9583JOVR/), [IGVFFI0287KKJM](/sequence-files/IGVFFI0287KKJM/) which do not have any `seqspecs`. Sequence files in a file set are expected to link to a sequence specification file.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_missing_seqspec",
"path": "/auxiliary-sets/IGVFDS3701EFIG/"
}
]
},
"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": "2024-08-16T20:05:28.072744+00:00",
"donors": [
{
"@id": "/human-donors/IGVFDO1756PPKO/",
"accession": "IGVFDO1756PPKO",
"aliases": [
"igvf:donor_of_WTC11"
],
"sex": "male",
"status": "released",
"taxa": "Homo sapiens"
}
],
"file_set_type": "cell hashing barcode sequencing",
"files": [
{
"@id": "/sequence-files/IGVFFI2410SQSR/",
"accession": "IGVFFI2410SQSR",
"aliases": [
"gary-hon:LW438C_6_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-13T20:00:33.887059+00:00",
"file_format": "fastq",
"file_size": 382408753,
"href": "/sequence-files/IGVFFI2410SQSR/@@download/IGVFFI2410SQSR.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/13/05913f57-dc4f-4586-b591-6eea8390391a/IGVFFI2410SQSR.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008637/",
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2024/2024-05-01-Novogene-NovaSeq.Hon19_20/HTO//LW438C_S32_L006_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9959PZPC/",
"accession": "IGVFFI9959PZPC",
"aliases": [
"gary-hon:LW438C_6_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-13T20:00:48.458459+00:00",
"file_format": "fastq",
"file_size": 421687350,
"href": "/sequence-files/IGVFFI9959PZPC/@@download/IGVFFI9959PZPC.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/13/43f2a5b1-f3e8-4e99-ab47-85e0c788a484/IGVFFI9959PZPC.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008637/",
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2024/2024-05-01-Novogene-NovaSeq.Hon19_20/HTO//LW438C_S32_L006_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9583JOVR/",
"accession": "IGVFFI9583JOVR",
"aliases": [
"gary-hon:LW438C_6_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-13T20:01:50.190149+00:00",
"file_format": "fastq",
"file_size": 4341620629,
"href": "/sequence-files/IGVFFI9583JOVR/@@download/IGVFFI9583JOVR.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/13/8387dfe1-32ee-4074-ab1d-87acb51ad7e2/IGVFFI9583JOVR.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008637/",
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2024/2024-05-01-Novogene-NovaSeq.Hon19_20/HTO//LW438C_S32_L006_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0287KKJM/",
"accession": "IGVFFI0287KKJM",
"aliases": [
"gary-hon:LW438C_6_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-13T20:01:03.385863+00:00",
"file_format": "fastq",
"file_size": 4045769066,
"href": "/sequence-files/IGVFFI0287KKJM/@@download/IGVFFI0287KKJM.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/13/e05c06b4-3088-4e78-9f71-adb1c0052063/IGVFFI0287KKJM.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008637/",
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2024/2024-05-01-Novogene-NovaSeq.Hon19_20/HTO//LW438C_S32_L006_R1_001.fastq.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS4252LFRU/"
],
"lab": {
"@id": "/labs/gary-hon/",
"title": "Gary Hon, UT"
},
"measurement_sets": [
{
"@id": "/measurement-sets/IGVFDS0961NLGM/",
"accession": "IGVFDS0961NLGM",
"aliases": [
"gary-hon:differentited_WTC11_CM_Pilot2_Mini_PB9_LW438"
],
"preferred_assay_title": "Perturb-seq",
"status": "preview"
}
],
"samples": [
{
"@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": "12",
"status": "preview",
"submitted_by": {
"@id": "/users/b05645f1-2d56-4a5e-b272-4601e555a3fa/",
"title": "Mpathi Nzima"
},
"submitted_files_timestamp": "2024-11-13T20:00:33.887059+00:00",
"summary": "cell hashing barcode sequencing for CRISPR interference Perturb-seq integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"uuid": "7170e47d-613f-463a-9730-77b4e2a61e51"
}