{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS2333GHSM/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS2333GHSM",
"aliases": [
"gary-hon:CM_Pilot_2_PB_sgRNA_LW233"
],
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS2333GHSM](/auxiliary-sets/IGVFDS2333GHSM/) has sequence file(s) [IGVFFI1584GGDI](/sequence-files/IGVFFI1584GGDI/), [IGVFFI2281VAEQ](/sequence-files/IGVFFI2281VAEQ/), [IGVFFI1706QJEX](/sequence-files/IGVFFI1706QJEX/), [IGVFFI5770WTCG](/sequence-files/IGVFFI5770WTCG/), [IGVFFI7279SSPT](/sequence-files/IGVFFI7279SSPT/), [IGVFFI5345XBBP](/sequence-files/IGVFFI5345XBBP/), [IGVFFI6506QHJL](/sequence-files/IGVFFI6506QHJL/), [IGVFFI4697NIDB](/sequence-files/IGVFFI4697NIDB/) 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/IGVFDS2333GHSM/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS2333GHSM](/auxiliary-sets/IGVFDS2333GHSM/) has sequence file(s): [IGVFFI1584GGDI](/sequence-files/IGVFFI1584GGDI/), [IGVFFI2281VAEQ](/sequence-files/IGVFFI2281VAEQ/), [IGVFFI1706QJEX](/sequence-files/IGVFFI1706QJEX/), [IGVFFI5770WTCG](/sequence-files/IGVFFI5770WTCG/), [IGVFFI7279SSPT](/sequence-files/IGVFFI7279SSPT/), [IGVFFI5345XBBP](/sequence-files/IGVFFI5345XBBP/), [IGVFFI6506QHJL](/sequence-files/IGVFFI6506QHJL/), [IGVFFI4697NIDB](/sequence-files/IGVFFI4697NIDB/) 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/IGVFDS2333GHSM/"
}
]
},
"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": "2024-02-15T23:35:36.600360+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": "IGVFFI1584GGDI",
"aliases": [
"gary-hon:LW233B-2_1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-21T18:22:19.115452+00:00",
"file_format": "fastq",
"file_size": 1219555267,
"href": "/sequence-files/IGVFFI1584GGDI/@@download/IGVFFI1584GGDI.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/21/0e828449-3f45-4050-9590-4fbb45392d11/IGVFFI1584GGDI.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/LW233B-2_S3_L001_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2281VAEQ/",
"accession": "IGVFFI2281VAEQ",
"aliases": [
"gary-hon:LW233B-2_2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-21T18:23:05.676825+00:00",
"file_format": "fastq",
"file_size": 1121793928,
"href": "/sequence-files/IGVFFI2281VAEQ/@@download/IGVFFI2281VAEQ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/21/3c6bab8c-cafa-4069-9e0e-16c188334583/IGVFFI2281VAEQ.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/LW233B-2_S3_L002_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1706QJEX/",
"accession": "IGVFFI1706QJEX",
"aliases": [
"gary-hon:LW233B-2_1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-21T18:22:05.042900+00:00",
"file_format": "fastq",
"file_size": 353928512,
"href": "/sequence-files/IGVFFI1706QJEX/@@download/IGVFFI1706QJEX.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/21/e32b3c59-da20-4e4a-9234-aa027964722b/IGVFFI1706QJEX.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/LW233B-2_S3_L001_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5770WTCG/",
"accession": "IGVFFI5770WTCG",
"aliases": [
"gary-hon:LW233B-2_1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-21T18:22:12.014180+00:00",
"file_format": "fastq",
"file_size": 375620867,
"href": "/sequence-files/IGVFFI5770WTCG/@@download/IGVFFI5770WTCG.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/21/b309a8ac-f5f0-414e-8d04-04f7d4404bbc/IGVFFI5770WTCG.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/LW233B-2_S3_L001_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7279SSPT/",
"accession": "IGVFFI7279SSPT",
"aliases": [
"gary-hon:LW233B-2_2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-21T18:22:51.643545+00:00",
"file_format": "fastq",
"file_size": 323045420,
"href": "/sequence-files/IGVFFI7279SSPT/@@download/IGVFFI7279SSPT.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/21/8eaf5923-a90f-4edc-a322-96af3ef3988f/IGVFFI7279SSPT.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/LW233B-2_S3_L002_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5345XBBP/",
"accession": "IGVFFI5345XBBP",
"aliases": [
"gary-hon:LW233B-2_2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-21T18:23:19.663051+00:00",
"file_format": "fastq",
"file_size": 1464033985,
"href": "/sequence-files/IGVFFI5345XBBP/@@download/IGVFFI5345XBBP.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/21/151c4e0a-c6e1-466c-bef0-5c63211073ba/IGVFFI5345XBBP.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/LW233B-2_S3_L002_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6506QHJL/",
"accession": "IGVFFI6506QHJL",
"aliases": [
"gary-hon:LW233B-2_1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-21T18:22:33.770233+00:00",
"file_format": "fastq",
"file_size": 1602864268,
"href": "/sequence-files/IGVFFI6506QHJL/@@download/IGVFFI6506QHJL.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/21/c814fe92-3356-4239-afd2-ec0e2f494e02/IGVFFI6506QHJL.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/LW233B-2_S3_L001_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4697NIDB/",
"accession": "IGVFFI4697NIDB",
"aliases": [
"gary-hon:LW233B-2_2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-21T18:22:58.646907+00:00",
"file_format": "fastq",
"file_size": 343518947,
"href": "/sequence-files/IGVFFI4697NIDB/@@download/IGVFFI4697NIDB.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/21/1330bf7f-920a-4627-a651-d33c972b10c7/IGVFFI4697NIDB.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/LW233B-2_S3_L002_I2_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/IGVFDS4323LXLZ/",
"accession": "IGVFDS4323LXLZ",
"aliases": [
"gary-hon:CM_Pilot_2_PB_RNA_LW233"
],
"preferred_assay_title": "Perturb-seq",
"status": "preview"
}
],
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM9371INZC/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM9371INZC",
"aliases": [
"nikhil-munshi:differentited_WTC11_CM_Pilot1_PB_LW233"
],
"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, 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": "2024-02-21T18:22:05.042900+00:00",
"summary": "gRNA sequencing for CRISPR interference Perturb-seq integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"uuid": "0d10eab9-5001-4889-b244-aab76832c8a6"
}