{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS1128FXRR/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS1128FXRR",
"aliases": [
"gary-hon:TF_Perturb_Seq_Pilot_Lenti_iPSC_sgRNA_LW286"
],
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS1128FXRR](/auxiliary-sets/IGVFDS1128FXRR/) has sequence file(s) [IGVFFI9511EKXQ](/sequence-files/IGVFFI9511EKXQ/), [IGVFFI6053YIFW](/sequence-files/IGVFFI6053YIFW/), [IGVFFI6212DKTA](/sequence-files/IGVFFI6212DKTA/), [IGVFFI6700ENLR](/sequence-files/IGVFFI6700ENLR/) 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/IGVFDS1128FXRR/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS1128FXRR](/auxiliary-sets/IGVFDS1128FXRR/) has sequence file(s): [IGVFFI9511EKXQ](/sequence-files/IGVFFI9511EKXQ/), [IGVFFI6053YIFW](/sequence-files/IGVFFI6053YIFW/), [IGVFFI6212DKTA](/sequence-files/IGVFFI6212DKTA/), [IGVFFI6700ENLR](/sequence-files/IGVFFI6700ENLR/) 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/IGVFDS1128FXRR/"
}
]
},
"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": "2024-02-21T21:22:36.367875+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/IGVFFI9511EKXQ/",
"accession": "IGVFFI9511EKXQ",
"aliases": [
"gary-hon:LW286B_1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-04T20:03:07.007618+00:00",
"file_format": "fastq",
"file_size": 394379201,
"href": "/sequence-files/IGVFFI9511EKXQ/@@download/IGVFFI9511EKXQ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/04/facf0d91-66ea-438a-8f4e-140a2e3f0d40/IGVFFI9511EKXQ.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//LW286B_S1_L001_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6053YIFW/",
"accession": "IGVFFI6053YIFW",
"aliases": [
"gary-hon:LW286B_1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-04T20:03:30.037500+00:00",
"file_format": "fastq",
"file_size": 1442041887,
"href": "/sequence-files/IGVFFI6053YIFW/@@download/IGVFFI6053YIFW.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/04/aa631f16-a865-4a04-9c3b-91897a23a4b2/IGVFFI6053YIFW.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//LW286B_S1_L001_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6212DKTA/",
"accession": "IGVFFI6212DKTA",
"aliases": [
"gary-hon:LW286B_1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-04T20:02:59.828176+00:00",
"file_format": "fastq",
"file_size": 370713206,
"href": "/sequence-files/IGVFFI6212DKTA/@@download/IGVFFI6212DKTA.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/04/17fed53b-ab45-441e-8c8a-5753532762d8/IGVFFI6212DKTA.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//LW286B_S1_L001_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6700ENLR/",
"accession": "IGVFFI6700ENLR",
"aliases": [
"gary-hon:LW286B_1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-04T20:03:14.320233+00:00",
"file_format": "fastq",
"file_size": 1360228226,
"href": "/sequence-files/IGVFFI6700ENLR/@@download/IGVFFI6700ENLR.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/04/93f5b77b-3c82-4244-9cb4-befc5a7c5bbe/IGVFFI6700ENLR.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//LW286B_S1_L001_R1_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/IGVFDS5429CXNB/",
"accession": "IGVFDS5429CXNB",
"aliases": [
"gary-hon:TF_Perturb_Seq_Pilot_Lenti_iPSC_LW286"
],
"preferred_assay_title": "Perturb-seq",
"status": "preview"
}
],
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM2726ORRN/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM2726ORRN",
"aliases": [
"nikhil-munshi:differentited_WTC11_TF_Perturb_Seq_Pilot_iPSC_Lenti_LW286"
],
"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_LW286), 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": "2024-03-04T20:02:59.828176+00:00",
"summary": "gRNA sequencing for CRISPR interference Perturb-seq integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"uuid": "c11b3cdb-416d-4dbd-8670-a52e872c3e5b"
}