{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS1931QVXR/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS1931QVXR",
"aliases": [
"gary-hon:TF_Perturb_Seq_Pilot_Lenti_iPSC_sgRNA_LW289"
],
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS1931QVXR](/auxiliary-sets/IGVFDS1931QVXR/) has sequence file(s) [IGVFFI2505GTMO](/sequence-files/IGVFFI2505GTMO/), [IGVFFI6068UCJF](/sequence-files/IGVFFI6068UCJF/), [IGVFFI1333KJVP](/sequence-files/IGVFFI1333KJVP/), [IGVFFI4370ZHGH](/sequence-files/IGVFFI4370ZHGH/) 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/IGVFDS1931QVXR/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS1931QVXR](/auxiliary-sets/IGVFDS1931QVXR/) has sequence file(s): [IGVFFI2505GTMO](/sequence-files/IGVFFI2505GTMO/), [IGVFFI6068UCJF](/sequence-files/IGVFFI6068UCJF/), [IGVFFI1333KJVP](/sequence-files/IGVFFI1333KJVP/), [IGVFFI4370ZHGH](/sequence-files/IGVFFI4370ZHGH/) 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/IGVFDS1931QVXR/"
}
]
},
"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": "2024-02-21T21:22:44.090120+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/IGVFFI2505GTMO/",
"accession": "IGVFFI2505GTMO",
"aliases": [
"gary-hon:LW289B_1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-04T20:06:33.667988+00:00",
"file_format": "fastq",
"file_size": 935770104,
"href": "/sequence-files/IGVFFI2505GTMO/@@download/IGVFFI2505GTMO.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/04/17eec6b0-32af-45d7-9027-6da89f2b8d43/IGVFFI2505GTMO.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//LW289B_S4_L001_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6068UCJF/",
"accession": "IGVFFI6068UCJF",
"aliases": [
"gary-hon:LW289B_1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-04T20:06:21.236562+00:00",
"file_format": "fastq",
"file_size": 300924967,
"href": "/sequence-files/IGVFFI6068UCJF/@@download/IGVFFI6068UCJF.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/04/17c5715d-379e-4396-9ef0-c81584df7334/IGVFFI6068UCJF.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//LW289B_S4_L001_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1333KJVP/",
"accession": "IGVFFI1333KJVP",
"aliases": [
"gary-hon:LW289B_1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-04T20:06:45.421760+00:00",
"file_format": "fastq",
"file_size": 989176168,
"href": "/sequence-files/IGVFFI1333KJVP/@@download/IGVFFI1333KJVP.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/04/d87044b9-175a-4a57-a257-6ae203cdea41/IGVFFI1333KJVP.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//LW289B_S4_L001_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4370ZHGH/",
"accession": "IGVFFI4370ZHGH",
"aliases": [
"gary-hon:LW289B_1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-04T20:06:27.679894+00:00",
"file_format": "fastq",
"file_size": 254620468,
"href": "/sequence-files/IGVFFI4370ZHGH/@@download/IGVFFI4370ZHGH.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/04/744c3ec5-71b8-47e1-935f-34899d6d3621/IGVFFI4370ZHGH.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//LW289B_S4_L001_I2_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/IGVFDS3495FUIW/",
"accession": "IGVFDS3495FUIW",
"aliases": [
"gary-hon:TF_Perturb_Seq_Pilot_Lenti_iPSC_LW289"
],
"preferred_assay_title": "Perturb-seq",
"status": "preview"
}
],
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM1597KVRS/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM1597KVRS",
"aliases": [
"nikhil-munshi:differentited_WTC11_TF_Perturb_Seq_Pilot_iPSC_Lenti_LW289"
],
"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_LW289), 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": "2024-03-04T20:06:21.236562+00:00",
"summary": "gRNA sequencing for CRISPR interference Perturb-seq integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"uuid": "6971de37-ca08-4bd1-994c-fb3bb01afd1c"
}