{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS3212YIVB/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS3212YIVB",
"aliases": [
"gary-hon:CM_Pilot_2_PB_sgRNA_LW237"
],
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS3212YIVB](/auxiliary-sets/IGVFDS3212YIVB/) has sequence file(s) [IGVFFI9859AZBM](/sequence-files/IGVFFI9859AZBM/), [IGVFFI8394REEI](/sequence-files/IGVFFI8394REEI/), [IGVFFI5714GMWE](/sequence-files/IGVFFI5714GMWE/), [IGVFFI9059QESJ](/sequence-files/IGVFFI9059QESJ/), [IGVFFI8864XBJJ](/sequence-files/IGVFFI8864XBJJ/), [IGVFFI6690RGJL](/sequence-files/IGVFFI6690RGJL/), [IGVFFI1258HMIV](/sequence-files/IGVFFI1258HMIV/), [IGVFFI1304WFWQ](/sequence-files/IGVFFI1304WFWQ/) which lack specification of a `sequencing_kit`. Sequence files should specify a sequencing kit.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_inconsistent_sequencing_kit",
"path": "/auxiliary-sets/IGVFDS3212YIVB/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS3212YIVB](/auxiliary-sets/IGVFDS3212YIVB/) has sequence file(s): [IGVFFI9859AZBM](/sequence-files/IGVFFI9859AZBM/), [IGVFFI8394REEI](/sequence-files/IGVFFI8394REEI/), [IGVFFI5714GMWE](/sequence-files/IGVFFI5714GMWE/), [IGVFFI9059QESJ](/sequence-files/IGVFFI9059QESJ/), [IGVFFI8864XBJJ](/sequence-files/IGVFFI8864XBJJ/), [IGVFFI6690RGJL](/sequence-files/IGVFFI6690RGJL/), [IGVFFI1258HMIV](/sequence-files/IGVFFI1258HMIV/), [IGVFFI1304WFWQ](/sequence-files/IGVFFI1304WFWQ/) 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/IGVFDS3212YIVB/"
}
]
},
"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": "2024-02-15T23:35:46.082251+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": [
{
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"accession": "IGVFFI9859AZBM",
"aliases": [
"gary-hon:LW237B-2_2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-21T18:32:32.741187+00:00",
"file_format": "fastq",
"file_size": 343487254,
"href": "/sequence-files/IGVFFI9859AZBM/@@download/IGVFFI9859AZBM.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/21/ce2be0e3-8ebc-4b3c-997e-7a09419d362c/IGVFFI9859AZBM.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0010963/",
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-03-24-McDermott-NextSeq.10X/2023-03-24/outs/fastq_path/AAC235NHV/LW237B-2_S7_L002_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8394REEI/",
"accession": "IGVFFI8394REEI",
"aliases": [
"gary-hon:LW237B-2_1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-21T18:31:32.085712+00:00",
"file_format": "fastq",
"file_size": 454647507,
"href": "/sequence-files/IGVFFI8394REEI/@@download/IGVFFI8394REEI.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/21/5c10a9f4-01dc-4415-900a-7ddb7af2949b/IGVFFI8394REEI.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0010963/",
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-03-24-McDermott-NextSeq.10X/2023-03-24/outs/fastq_path/AAC235NHV/LW237B-2_S7_L001_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5714GMWE/",
"accession": "IGVFFI5714GMWE",
"aliases": [
"gary-hon:LW237B-2_1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-21T18:32:05.505908+00:00",
"file_format": "fastq",
"file_size": 1727893849,
"href": "/sequence-files/IGVFFI5714GMWE/@@download/IGVFFI5714GMWE.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/21/25ce7738-a703-4d19-9ce0-7b73155f8e49/IGVFFI5714GMWE.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0010963/",
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-03-24-McDermott-NextSeq.10X/2023-03-24/outs/fastq_path/AAC235NHV/LW237B-2_S7_L001_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9059QESJ/",
"accession": "IGVFFI9059QESJ",
"aliases": [
"gary-hon:LW237B-2_2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-21T18:32:24.563760+00:00",
"file_format": "fastq",
"file_size": 445032375,
"href": "/sequence-files/IGVFFI9059QESJ/@@download/IGVFFI9059QESJ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/21/7e15e626-b966-4b98-a23c-ca27132cdf14/IGVFFI9059QESJ.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0010963/",
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-03-24-McDermott-NextSeq.10X/2023-03-24/outs/fastq_path/AAC235NHV/LW237B-2_S7_L002_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8864XBJJ/",
"accession": "IGVFFI8864XBJJ",
"aliases": [
"gary-hon:LW237B-2_1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-21T18:31:48.183205+00:00",
"file_format": "fastq",
"file_size": 1320352791,
"href": "/sequence-files/IGVFFI8864XBJJ/@@download/IGVFFI8864XBJJ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/21/a554a60c-5462-426c-a871-886440890353/IGVFFI8864XBJJ.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0010963/",
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-03-24-McDermott-NextSeq.10X/2023-03-24/outs/fastq_path/AAC235NHV/LW237B-2_S7_L001_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6690RGJL/",
"accession": "IGVFFI6690RGJL",
"aliases": [
"gary-hon:LW237B-2_2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-21T18:32:56.114985+00:00",
"file_format": "fastq",
"file_size": 1671288667,
"href": "/sequence-files/IGVFFI6690RGJL/@@download/IGVFFI6690RGJL.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/21/0ffa3a76-76b7-4a65-a359-ccdca27627cb/IGVFFI6690RGJL.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0010963/",
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-03-24-McDermott-NextSeq.10X/2023-03-24/outs/fastq_path/AAC235NHV/LW237B-2_S7_L002_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1258HMIV/",
"accession": "IGVFFI1258HMIV",
"aliases": [
"gary-hon:LW237B-2_1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-21T18:31:40.587260+00:00",
"file_format": "fastq",
"file_size": 367732662,
"href": "/sequence-files/IGVFFI1258HMIV/@@download/IGVFFI1258HMIV.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/21/d1c0709d-3d2c-475d-aa3b-d68aac1baba9/IGVFFI1258HMIV.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0010963/",
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-03-24-McDermott-NextSeq.10X/2023-03-24/outs/fastq_path/AAC235NHV/LW237B-2_S7_L001_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1304WFWQ/",
"accession": "IGVFFI1304WFWQ",
"aliases": [
"gary-hon:LW237B-2_2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-21T18:32:40.457290+00:00",
"file_format": "fastq",
"file_size": 1284777380,
"href": "/sequence-files/IGVFFI1304WFWQ/@@download/IGVFFI1304WFWQ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/21/d32045d4-cb28-411d-8e6c-ad30bd730887/IGVFFI1304WFWQ.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0010963/",
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-03-24-McDermott-NextSeq.10X/2023-03-24/outs/fastq_path/AAC235NHV/LW237B-2_S7_L002_R1_001.fastq.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS9192YMGI/"
],
"lab": {
"@id": "/labs/gary-hon/",
"title": "Gary Hon, UT"
},
"measurement_sets": [
{
"@id": "/measurement-sets/IGVFDS2593KURF/",
"accession": "IGVFDS2593KURF",
"aliases": [
"gary-hon:CM_Pilot_2_PB_RNA_LW237"
],
"preferred_assay_title": "Perturb-seq",
"status": "preview"
}
],
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM2329UXLZ/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM2329UXLZ",
"aliases": [
"nikhil-munshi:differentited_WTC11_CM_Pilot1_PB_LW237"
],
"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, 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": "2024-02-21T18:31:32.085712+00:00",
"summary": "gRNA sequencing for CRISPR interference Perturb-seq integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"uuid": "c96d1c7f-3166-471b-aafc-744c1458bee1"
}