{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS3881UZJT/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS3881UZJT",
"aliases": [
"gary-hon:differentited_WTC11_CM_Pilot2_Mini_PB9_sgRNA_LW435"
],
"audit": {
"ERROR": [
{
"category": "inconsistent sequencing kit",
"detail": "Auxiliary set [IGVFDS3881UZJT](/auxiliary-sets/IGVFDS3881UZJT/) has a sequence file [IGVFFI8257WJQZ](/sequence-files/IGVFFI8257WJQZ/) 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/IGVFDS3881UZJT/"
},
{
"category": "inconsistent sequencing kit",
"detail": "Auxiliary set [IGVFDS3881UZJT](/auxiliary-sets/IGVFDS3881UZJT/) has a sequence file [IGVFFI7650HNVF](/sequence-files/IGVFFI7650HNVF/) 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/IGVFDS3881UZJT/"
},
{
"category": "inconsistent sequencing kit",
"detail": "Auxiliary set [IGVFDS3881UZJT](/auxiliary-sets/IGVFDS3881UZJT/) has a sequence file [IGVFFI5492QZLT](/sequence-files/IGVFFI5492QZLT/) 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/IGVFDS3881UZJT/"
},
{
"category": "inconsistent sequencing kit",
"detail": "Auxiliary set [IGVFDS3881UZJT](/auxiliary-sets/IGVFDS3881UZJT/) has a sequence file [IGVFFI5457CMID](/sequence-files/IGVFFI5457CMID/) 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/IGVFDS3881UZJT/"
}
],
"INTERNAL_ACTION": [
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS3881UZJT](/auxiliary-sets/IGVFDS3881UZJT/) has sequence file(s): [IGVFFI8257WJQZ](/sequence-files/IGVFFI8257WJQZ/), [IGVFFI7650HNVF](/sequence-files/IGVFFI7650HNVF/), [IGVFFI5492QZLT](/sequence-files/IGVFFI5492QZLT/), [IGVFFI5457CMID](/sequence-files/IGVFFI5457CMID/) 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/IGVFDS3881UZJT/"
}
]
},
"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": "2024-08-16T20:05:21.815920+00:00",
"donors": [
{
"@id": "/human-donors/IGVFDO1756PPKO/",
"accession": "IGVFDO1756PPKO",
"aliases": [
"igvf:donor_of_WTC11"
],
"sex": "male",
"status": "released",
"taxa": "Homo sapiens"
}
],
"file_set_type": "gRNA sequencing",
"files": [
{
"@id": "/sequence-files/IGVFFI8257WJQZ/",
"accession": "IGVFFI8257WJQZ",
"aliases": [
"gary-hon:LW435B_6_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-13T20:04:32.045818+00:00",
"file_format": "fastq",
"file_size": 6489149748,
"href": "/sequence-files/IGVFFI8257WJQZ/@@download/IGVFFI8257WJQZ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/13/49dc139b-1421-49ff-bf62-15994a91eff5/IGVFFI8257WJQZ.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//LW435B_S9_L006_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7650HNVF/",
"accession": "IGVFFI7650HNVF",
"aliases": [
"gary-hon:LW435B_6_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-13T20:02:39.019638+00:00",
"file_format": "fastq",
"file_size": 840814521,
"href": "/sequence-files/IGVFFI7650HNVF/@@download/IGVFFI7650HNVF.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/13/26654a9f-af35-4283-a298-15a662013eb5/IGVFFI7650HNVF.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//LW435B_S9_L006_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5492QZLT/",
"accession": "IGVFFI5492QZLT",
"aliases": [
"gary-hon:LW435B_6_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-13T20:03:00.714541+00:00",
"file_format": "fastq",
"file_size": 859235372,
"href": "/sequence-files/IGVFFI5492QZLT/@@download/IGVFFI5492QZLT.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/13/d5d1b65d-c455-49b4-9669-9bd7e3032e22/IGVFFI5492QZLT.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//LW435B_S9_L006_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5457CMID/",
"accession": "IGVFFI5457CMID",
"aliases": [
"gary-hon:LW435B_6_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-13T20:03:22.287668+00:00",
"file_format": "fastq",
"file_size": 6548086631,
"href": "/sequence-files/IGVFFI5457CMID/@@download/IGVFFI5457CMID.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/13/237adac3-a015-4632-b015-cba173364049/IGVFFI5457CMID.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//LW435B_S9_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/IGVFDS7818HFMO/",
"accession": "IGVFDS7818HFMO",
"aliases": [
"gary-hon:differentited_WTC11_CM_Pilot2_Mini_PB9_LW435"
],
"preferred_assay_title": "Perturb-seq",
"status": "preview"
}
],
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM4418NJET/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM4418NJET",
"aliases": [
"nikhil-munshi:differentited_WTC11_CM_Pilot2_Mini_PB9_LW435"
],
"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_LW435), 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": "2024-11-13T20:02:39.019638+00:00",
"summary": "gRNA sequencing for CRISPR interference Perturb-seq integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"uuid": "e81a0f7d-930d-430b-a13e-8e07e59bfb08"
}