{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS6503WNZT/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS6503WNZT",
"aliases": [
"gary-hon:TF_Perturb_Seq_Pilot_Lenti_iPSC_sgRNA_LW288"
],
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS6503WNZT](/auxiliary-sets/IGVFDS6503WNZT/) has sequence file(s) [IGVFFI8822WNTR](/sequence-files/IGVFFI8822WNTR/), [IGVFFI9641ZDCL](/sequence-files/IGVFFI9641ZDCL/), [IGVFFI0507ZCWD](/sequence-files/IGVFFI0507ZCWD/), [IGVFFI8913KNGR](/sequence-files/IGVFFI8913KNGR/) 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/IGVFDS6503WNZT/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS6503WNZT](/auxiliary-sets/IGVFDS6503WNZT/) has sequence file(s): [IGVFFI8822WNTR](/sequence-files/IGVFFI8822WNTR/), [IGVFFI9641ZDCL](/sequence-files/IGVFFI9641ZDCL/), [IGVFFI0507ZCWD](/sequence-files/IGVFFI0507ZCWD/), [IGVFFI8913KNGR](/sequence-files/IGVFFI8913KNGR/) 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/IGVFDS6503WNZT/"
}
]
},
"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": "2024-02-21T21:22:41.769178+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/IGVFFI8822WNTR/",
"accession": "IGVFFI8822WNTR",
"aliases": [
"gary-hon:LW288B_1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-04T20:05:15.068721+00:00",
"file_format": "fastq",
"file_size": 276529736,
"href": "/sequence-files/IGVFFI8822WNTR/@@download/IGVFFI8822WNTR.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/04/3532bce0-1ca5-45db-93ac-5d6c3c0675d6/IGVFFI8822WNTR.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//LW288B_S3_L001_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9641ZDCL/",
"accession": "IGVFFI9641ZDCL",
"aliases": [
"gary-hon:LW288B_1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-04T20:05:40.948894+00:00",
"file_format": "fastq",
"file_size": 1159417938,
"href": "/sequence-files/IGVFFI9641ZDCL/@@download/IGVFFI9641ZDCL.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/04/65716722-71c6-4da3-a8f7-2f08d3390793/IGVFFI9641ZDCL.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//LW288B_S3_L001_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0507ZCWD/",
"accession": "IGVFFI0507ZCWD",
"aliases": [
"gary-hon:LW288B_1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-04T20:05:21.173869+00:00",
"file_format": "fastq",
"file_size": 309174699,
"href": "/sequence-files/IGVFFI0507ZCWD/@@download/IGVFFI0507ZCWD.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/04/8fbca3f8-f6d4-43d1-9609-9e746d7d7d90/IGVFFI0507ZCWD.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//LW288B_S3_L001_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8913KNGR/",
"accession": "IGVFFI8913KNGR",
"aliases": [
"gary-hon:LW288B_1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-04T20:05:27.625169+00:00",
"file_format": "fastq",
"file_size": 1094319853,
"href": "/sequence-files/IGVFFI8913KNGR/@@download/IGVFFI8913KNGR.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/04/3b2dd93d-6a48-4352-a474-bf2ce6dc9bec/IGVFFI8913KNGR.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//LW288B_S3_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/IGVFDS3975OFAO/",
"accession": "IGVFDS3975OFAO",
"aliases": [
"gary-hon:TF_Perturb_Seq_Pilot_Lenti_iPSC_LW288"
],
"preferred_assay_title": "Perturb-seq",
"status": "preview"
}
],
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM9411HZLU/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM9411HZLU",
"aliases": [
"nikhil-munshi:differentited_WTC11_TF_Perturb_Seq_Pilot_iPSC_Lenti_LW288"
],
"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_LW288), 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": "2024-03-04T20:05:15.068721+00:00",
"summary": "gRNA sequencing for CRISPR interference Perturb-seq integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"uuid": "f55baff0-9b49-4df0-afdf-1029e5bc940c"
}