{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS1937JPZI/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS1937JPZI",
"aliases": [
"gary-hon:TF_Perturb_Seq_Pilot_Lenti_iPSC_sgRNA_LW287"
],
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS1937JPZI](/auxiliary-sets/IGVFDS1937JPZI/) has sequence file(s) [IGVFFI8385HABJ](/sequence-files/IGVFFI8385HABJ/), [IGVFFI3275ZEBW](/sequence-files/IGVFFI3275ZEBW/), [IGVFFI1518BMVF](/sequence-files/IGVFFI1518BMVF/), [IGVFFI7286ZUUS](/sequence-files/IGVFFI7286ZUUS/) 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/IGVFDS1937JPZI/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS1937JPZI](/auxiliary-sets/IGVFDS1937JPZI/) has sequence file(s): [IGVFFI8385HABJ](/sequence-files/IGVFFI8385HABJ/), [IGVFFI3275ZEBW](/sequence-files/IGVFFI3275ZEBW/), [IGVFFI1518BMVF](/sequence-files/IGVFFI1518BMVF/), [IGVFFI7286ZUUS](/sequence-files/IGVFFI7286ZUUS/) 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/IGVFDS1937JPZI/"
}
]
},
"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": "2024-02-21T21:22:39.581301+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/IGVFFI8385HABJ/",
"accession": "IGVFFI8385HABJ",
"aliases": [
"gary-hon:LW287B_1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-04T20:04:12.498570+00:00",
"file_format": "fastq",
"file_size": 375700900,
"href": "/sequence-files/IGVFFI8385HABJ/@@download/IGVFFI8385HABJ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/04/f00dd93c-e367-4114-b933-fad67de66f67/IGVFFI8385HABJ.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0010963/",
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-11-03-McDermott-NextSeq.10X.run2.10X/2023-11-03/outs/fastq_path/AAF3JCVM5//LW287B_S2_L001_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3275ZEBW/",
"accession": "IGVFFI3275ZEBW",
"aliases": [
"gary-hon:LW287B_1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-04T20:04:34.151158+00:00",
"file_format": "fastq",
"file_size": 1296422121,
"href": "/sequence-files/IGVFFI3275ZEBW/@@download/IGVFFI3275ZEBW.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/04/f2cdf4bd-feb7-41e9-8e61-541ad7d989ac/IGVFFI3275ZEBW.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0010963/",
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-11-03-McDermott-NextSeq.10X.run2.10X/2023-11-03/outs/fastq_path/AAF3JCVM5//LW287B_S2_L001_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1518BMVF/",
"accession": "IGVFFI1518BMVF",
"aliases": [
"gary-hon:LW287B_1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-04T20:04:19.656655+00:00",
"file_format": "fastq",
"file_size": 1229341418,
"href": "/sequence-files/IGVFFI1518BMVF/@@download/IGVFFI1518BMVF.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/04/7170fbb6-dff0-4b57-8a43-7e727386d9a3/IGVFFI1518BMVF.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0010963/",
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-11-03-McDermott-NextSeq.10X.run2.10X/2023-11-03/outs/fastq_path/AAF3JCVM5//LW287B_S2_L001_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7286ZUUS/",
"accession": "IGVFFI7286ZUUS",
"aliases": [
"gary-hon:LW287B_1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-04T20:04:05.436529+00:00",
"file_format": "fastq",
"file_size": 369135930,
"href": "/sequence-files/IGVFFI7286ZUUS/@@download/IGVFFI7286ZUUS.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/04/1d415f05-b619-470c-bca5-6e6f3a5d2011/IGVFFI7286ZUUS.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0010963/",
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-11-03-McDermott-NextSeq.10X.run2.10X/2023-11-03/outs/fastq_path/AAF3JCVM5//LW287B_S2_L001_I1_001.fastq.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS7340YDHF/"
],
"lab": {
"@id": "/labs/gary-hon/",
"title": "Gary Hon, UT"
},
"measurement_sets": [
{
"@id": "/measurement-sets/IGVFDS2692VBHQ/",
"accession": "IGVFDS2692VBHQ",
"aliases": [
"gary-hon:TF_Perturb_Seq_Pilot_Lenti_iPSC_LW287"
],
"preferred_assay_title": "Perturb-seq",
"status": "preview"
}
],
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM1153INDY/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM1153INDY",
"aliases": [
"nikhil-munshi:differentited_WTC11_TF_Perturb_Seq_Pilot_iPSC_Lenti_LW287"
],
"classifications": [
"cell line"
],
"construct_library_sets": [
"/construct-library-sets/IGVFDS2302LCEO/"
],
"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) cell line (cellular sub pool: subpool_LW287), male, Homo sapiens modified with CRISPRi Sp-dCas9, transduced (lentivirus) with a guide library",
"taxa": "Homo sapiens"
}
],
"schema_version": "12",
"status": "preview",
"submitted_by": {
"@id": "/users/b05645f1-2d56-4a5e-b272-4601e555a3fa/",
"title": "Mpathi Nzima"
},
"submitted_files_timestamp": "2024-03-04T20:04:05.436529+00:00",
"summary": "gRNA sequencing for CRISPR interference Perturb-seq integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"uuid": "1de99972-e596-423e-84ad-0d3cf37bf659"
}