{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS3465KEWH/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS3465KEWH",
"aliases": [
"gary-hon:TF_Perturb_Seq_Pilot_Lenti_iPSC_HTO_LW286"
],
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS3465KEWH](/auxiliary-sets/IGVFDS3465KEWH/) has sequence file(s) [IGVFFI3046CEDS](/sequence-files/IGVFFI3046CEDS/), [IGVFFI2095GWCE](/sequence-files/IGVFFI2095GWCE/), [IGVFFI4014VOTR](/sequence-files/IGVFFI4014VOTR/), [IGVFFI6603ZNLC](/sequence-files/IGVFFI6603ZNLC/) 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/IGVFDS3465KEWH/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS3465KEWH](/auxiliary-sets/IGVFDS3465KEWH/) has sequence file(s): [IGVFFI3046CEDS](/sequence-files/IGVFFI3046CEDS/), [IGVFFI2095GWCE](/sequence-files/IGVFFI2095GWCE/), [IGVFFI4014VOTR](/sequence-files/IGVFFI4014VOTR/), [IGVFFI6603ZNLC](/sequence-files/IGVFFI6603ZNLC/) 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/IGVFDS3465KEWH/"
}
]
},
"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": "2024-02-21T21:22:37.791237+00:00",
"donors": [
{
"@id": "/human-donors/IGVFDO1756PPKO/",
"accession": "IGVFDO1756PPKO",
"aliases": [
"igvf:donor_of_WTC11"
],
"sex": "male",
"status": "released",
"taxa": "Homo sapiens"
}
],
"file_set_type": "cell hashing barcode sequencing",
"files": [
{
"@id": "/sequence-files/IGVFFI3046CEDS/",
"accession": "IGVFFI3046CEDS",
"aliases": [
"gary-hon:LW286C_1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-04T20:03:59.339508+00:00",
"file_format": "fastq",
"file_size": 258677637,
"href": "/sequence-files/IGVFFI3046CEDS/@@download/IGVFFI3046CEDS.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/04/3dc76a1f-534c-47c8-beb5-cdd004f6aecf/IGVFFI3046CEDS.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//LW286C_S5_L001_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2095GWCE/",
"accession": "IGVFFI2095GWCE",
"aliases": [
"gary-hon:LW286C_1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-04T20:03:46.139107+00:00",
"file_format": "fastq",
"file_size": 43260257,
"href": "/sequence-files/IGVFFI2095GWCE/@@download/IGVFFI2095GWCE.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/04/5233b62c-9305-413d-8773-da4ef8a15eeb/IGVFFI2095GWCE.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//LW286C_S5_L001_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4014VOTR/",
"accession": "IGVFFI4014VOTR",
"aliases": [
"gary-hon:LW286C_1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-04T20:03:50.221142+00:00",
"file_format": "fastq",
"file_size": 51112022,
"href": "/sequence-files/IGVFFI4014VOTR/@@download/IGVFFI4014VOTR.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/04/57790cdc-80bf-498d-bfd6-c9e28e4379b1/IGVFFI4014VOTR.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//LW286C_S5_L001_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6603ZNLC/",
"accession": "IGVFFI6603ZNLC",
"aliases": [
"gary-hon:LW286C_1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-04T20:03:54.413800+00:00",
"file_format": "fastq",
"file_size": 130696069,
"href": "/sequence-files/IGVFFI6603ZNLC/@@download/IGVFFI6603ZNLC.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/04/75129726-2a03-4ec8-8ccf-705b8a8aae1d/IGVFFI6603ZNLC.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//LW286C_S5_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"
}
],
"notes": "File_set_type enum cell hashing has been renamed to be cell hashing barcode sequencing.",
"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": "2024-03-04T20:03:46.139107+00:00",
"summary": "cell hashing barcode sequencing for CRISPR interference Perturb-seq integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"uuid": "ba93f970-aa8e-4e39-9d38-89526d6e31b2"
}