{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS5403GYDH/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS5403GYDH",
"aliases": [
"gary-hon:differentited_H9_CM_Pilot2_Mini_PB9_sgRNA_LW432"
],
"audit": {
"ERROR": [
{
"category": "inconsistent sequencing kit",
"detail": "Auxiliary set [IGVFDS5403GYDH](/auxiliary-sets/IGVFDS5403GYDH/) has a sequence file [IGVFFI2639TNEY](/sequence-files/IGVFFI2639TNEY/) 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/IGVFDS5403GYDH/"
},
{
"category": "inconsistent sequencing kit",
"detail": "Auxiliary set [IGVFDS5403GYDH](/auxiliary-sets/IGVFDS5403GYDH/) has a sequence file [IGVFFI0508AHMI](/sequence-files/IGVFFI0508AHMI/) 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/IGVFDS5403GYDH/"
},
{
"category": "inconsistent sequencing kit",
"detail": "Auxiliary set [IGVFDS5403GYDH](/auxiliary-sets/IGVFDS5403GYDH/) has a sequence file [IGVFFI7827HSIX](/sequence-files/IGVFFI7827HSIX/) 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/IGVFDS5403GYDH/"
},
{
"category": "inconsistent sequencing kit",
"detail": "Auxiliary set [IGVFDS5403GYDH](/auxiliary-sets/IGVFDS5403GYDH/) has a sequence file [IGVFFI1627XZSE](/sequence-files/IGVFFI1627XZSE/) 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/IGVFDS5403GYDH/"
}
],
"INTERNAL_ACTION": [
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS5403GYDH](/auxiliary-sets/IGVFDS5403GYDH/) has sequence file(s): [IGVFFI2639TNEY](/sequence-files/IGVFFI2639TNEY/), [IGVFFI0508AHMI](/sequence-files/IGVFFI0508AHMI/), [IGVFFI7827HSIX](/sequence-files/IGVFFI7827HSIX/), [IGVFFI1627XZSE](/sequence-files/IGVFFI1627XZSE/) 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/IGVFDS5403GYDH/"
}
]
},
"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": "2024-08-16T20:05:16.185953+00:00",
"donors": [
{
"@id": "/human-donors/IGVFDO2718IDDQ/",
"accession": "IGVFDO2718IDDQ",
"aliases": [
"igvf:donor_of_H9"
],
"sex": "female",
"status": "released",
"taxa": "Homo sapiens"
}
],
"file_set_type": "gRNA sequencing",
"files": [
{
"@id": "/sequence-files/IGVFFI2639TNEY/",
"accession": "IGVFFI2639TNEY",
"aliases": [
"gary-hon:LW432B_6_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-13T19:47:54.084196+00:00",
"file_format": "fastq",
"file_size": 6672840223,
"href": "/sequence-files/IGVFFI2639TNEY/@@download/IGVFFI2639TNEY.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/13/dc923ea8-15ff-4251-afe8-a48e8c76c086/IGVFFI2639TNEY.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/sgRNA//LW432B_S6_L006_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0508AHMI/",
"accession": "IGVFFI0508AHMI",
"aliases": [
"gary-hon:LW432B_6_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-13T19:46:46.600367+00:00",
"file_format": "fastq",
"file_size": 6705883231,
"href": "/sequence-files/IGVFFI0508AHMI/@@download/IGVFFI0508AHMI.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/13/33481e14-48c5-4e9c-a4d9-5d33dcf05a16/IGVFFI0508AHMI.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/sgRNA//LW432B_S6_L006_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7827HSIX/",
"accession": "IGVFFI7827HSIX",
"aliases": [
"gary-hon:LW432B_6_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-13T19:46:12.683418+00:00",
"file_format": "fastq",
"file_size": 853740423,
"href": "/sequence-files/IGVFFI7827HSIX/@@download/IGVFFI7827HSIX.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/13/b1cd2d33-d4e2-4bda-98e0-78dace08515d/IGVFFI7827HSIX.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/sgRNA//LW432B_S6_L006_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1627XZSE/",
"accession": "IGVFFI1627XZSE",
"aliases": [
"gary-hon:LW432B_6_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-13T19:46:29.086979+00:00",
"file_format": "fastq",
"file_size": 936111968,
"href": "/sequence-files/IGVFFI1627XZSE/@@download/IGVFFI1627XZSE.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/13/c65146eb-da7c-4c8e-9824-546d2bd5e34d/IGVFFI1627XZSE.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/sgRNA//LW432B_S6_L006_I2_001.fastq.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS2266YDVM/"
],
"lab": {
"@id": "/labs/gary-hon/",
"title": "Gary Hon, UT"
},
"measurement_sets": [
{
"@id": "/measurement-sets/IGVFDS8183DTKY/",
"accession": "IGVFDS8183DTKY",
"aliases": [
"gary-hon:differentited_H9_CM_Pilot2_Mini_PB9_LW432"
],
"preferred_assay_title": "Perturb-seq",
"status": "preview"
}
],
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM3839SOTK/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM3839SOTK",
"aliases": [
"nikhil-munshi:differentited_H9_CM_Pilot2_Mini_PB9_LW432"
],
"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_0003045/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"aliases": [
"igvf:H9"
],
"status": "released",
"summary": "H9",
"term_name": "H9"
}
],
"status": "preview",
"summary": "H9 differentiated cell specimen induced to cardiac muscle cell for 12 days (cellular sub pool: subpool_LW432), female, 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": "2024-11-13T19:46:12.683418+00:00",
"summary": "gRNA sequencing for CRISPR interference Perturb-seq integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"uuid": "14a0dd9c-f220-4ef8-b1a7-d75151f6b1c6"
}