{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS7027VRZT/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS7027VRZT",
"aliases": [
"gary-hon:TF_Perturb_Seq_Pilot_Lenti_CM_HTO_LW279"
],
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS7027VRZT](/auxiliary-sets/IGVFDS7027VRZT/) has sequence file(s) [IGVFFI1430HEKM](/sequence-files/IGVFFI1430HEKM/), [IGVFFI9545FKJR](/sequence-files/IGVFFI9545FKJR/), [IGVFFI8807NJZP](/sequence-files/IGVFFI8807NJZP/), [IGVFFI9254UKTW](/sequence-files/IGVFFI9254UKTW/), [IGVFFI1865XZZP](/sequence-files/IGVFFI1865XZZP/), [IGVFFI9553XEEI](/sequence-files/IGVFFI9553XEEI/), [IGVFFI8178OKCW](/sequence-files/IGVFFI8178OKCW/), [IGVFFI2898JUNF](/sequence-files/IGVFFI2898JUNF/) 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/IGVFDS7027VRZT/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS7027VRZT](/auxiliary-sets/IGVFDS7027VRZT/) has sequence file(s): [IGVFFI1430HEKM](/sequence-files/IGVFFI1430HEKM/), [IGVFFI9545FKJR](/sequence-files/IGVFFI9545FKJR/), [IGVFFI8807NJZP](/sequence-files/IGVFFI8807NJZP/), [IGVFFI9254UKTW](/sequence-files/IGVFFI9254UKTW/), [IGVFFI1865XZZP](/sequence-files/IGVFFI1865XZZP/), [IGVFFI9553XEEI](/sequence-files/IGVFFI9553XEEI/), [IGVFFI8178OKCW](/sequence-files/IGVFFI8178OKCW/), [IGVFFI2898JUNF](/sequence-files/IGVFFI2898JUNF/) 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/IGVFDS7027VRZT/"
}
]
},
"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": "2024-02-21T21:01:52.014079+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/IGVFFI1430HEKM/",
"accession": "IGVFFI1430HEKM",
"aliases": [
"gary-hon:LW279C_2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-01T17:12:32.046624+00:00",
"file_format": "fastq",
"file_size": 87832951,
"href": "/sequence-files/IGVFFI1430HEKM/@@download/IGVFFI1430HEKM.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/01/cb67c853-6e9c-40d5-9669-d9a1e35bd0ff/IGVFFI1430HEKM.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0010963/",
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-10-05-McDermott-NextSeq.10X/2023-10-05/outs/fastq_path/AAC7VLGHV/LW279C_S3_L002_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9545FKJR/",
"accession": "IGVFFI9545FKJR",
"aliases": [
"gary-hon:LW279C_1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-01T17:12:04.691771+00:00",
"file_format": "fastq",
"file_size": 92659770,
"href": "/sequence-files/IGVFFI9545FKJR/@@download/IGVFFI9545FKJR.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/01/d1480b6d-013d-4f4c-89f6-730b3d8e68c6/IGVFFI9545FKJR.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0010963/",
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-10-05-McDermott-NextSeq.10X/2023-10-05/outs/fastq_path/AAC7VLGHV/LW279C_S3_L001_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8807NJZP/",
"accession": "IGVFFI8807NJZP",
"aliases": [
"gary-hon:LW279C_1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-01T17:12:14.056573+00:00",
"file_format": "fastq",
"file_size": 243639357,
"href": "/sequence-files/IGVFFI8807NJZP/@@download/IGVFFI8807NJZP.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/01/30154924-6a44-475d-aa85-3e7179e0450c/IGVFFI8807NJZP.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0010963/",
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-10-05-McDermott-NextSeq.10X/2023-10-05/outs/fastq_path/AAC7VLGHV/LW279C_S3_L001_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9254UKTW/",
"accession": "IGVFFI9254UKTW",
"aliases": [
"gary-hon:LW279C_2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-01T17:12:27.529963+00:00",
"file_format": "fastq",
"file_size": 84309393,
"href": "/sequence-files/IGVFFI9254UKTW/@@download/IGVFFI9254UKTW.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/01/43c5f089-fb48-4d00-a341-ab0338af63e2/IGVFFI9254UKTW.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0010963/",
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-10-05-McDermott-NextSeq.10X/2023-10-05/outs/fastq_path/AAC7VLGHV/LW279C_S3_L002_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1865XZZP/",
"accession": "IGVFFI1865XZZP",
"aliases": [
"gary-hon:LW279C_2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-01T17:12:36.608990+00:00",
"file_format": "fastq",
"file_size": 219195702,
"href": "/sequence-files/IGVFFI1865XZZP/@@download/IGVFFI1865XZZP.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/01/6d5c9984-cafe-427c-a06e-8d6522c49613/IGVFFI1865XZZP.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0010963/",
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-10-05-McDermott-NextSeq.10X/2023-10-05/outs/fastq_path/AAC7VLGHV/LW279C_S3_L002_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9553XEEI/",
"accession": "IGVFFI9553XEEI",
"aliases": [
"gary-hon:LW279C_2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-01T17:12:42.354916+00:00",
"file_format": "fastq",
"file_size": 427005579,
"href": "/sequence-files/IGVFFI9553XEEI/@@download/IGVFFI9553XEEI.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/01/580c85da-b7ee-46f2-b93c-c98a74106f54/IGVFFI9553XEEI.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0010963/",
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-10-05-McDermott-NextSeq.10X/2023-10-05/outs/fastq_path/AAC7VLGHV/LW279C_S3_L002_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8178OKCW/",
"accession": "IGVFFI8178OKCW",
"aliases": [
"gary-hon:LW279C_1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-01T17:12:09.336629+00:00",
"file_format": "fastq",
"file_size": 96437046,
"href": "/sequence-files/IGVFFI8178OKCW/@@download/IGVFFI8178OKCW.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/01/64a419ab-204d-4528-a8c2-34b66e532509/IGVFFI8178OKCW.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0010963/",
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-10-05-McDermott-NextSeq.10X/2023-10-05/outs/fastq_path/AAC7VLGHV/LW279C_S3_L001_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2898JUNF/",
"accession": "IGVFFI2898JUNF",
"aliases": [
"gary-hon:LW279C_1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-01T17:12:19.801947+00:00",
"file_format": "fastq",
"file_size": 476419277,
"href": "/sequence-files/IGVFFI2898JUNF/@@download/IGVFFI2898JUNF.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/01/6e1d3500-d51d-4230-8bf7-0ae848cf4a76/IGVFFI2898JUNF.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0010963/",
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-10-05-McDermott-NextSeq.10X/2023-10-05/outs/fastq_path/AAC7VLGHV/LW279C_S3_L001_R2_001.fastq.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS4389OUWU/"
],
"lab": {
"@id": "/labs/gary-hon/",
"title": "Gary Hon, UT"
},
"measurement_sets": [
{
"@id": "/measurement-sets/IGVFDS7733OTCA/",
"accession": "IGVFDS7733OTCA",
"aliases": [
"gary-hon:TF_Perturb_Seq_Pilot_Lenti_CM_LW279"
],
"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/IGVFSM0559UNMK/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM0559UNMK",
"aliases": [
"nikhil-munshi:differentited_WTC11_TF_Perturb_Seq_Pilot_CMs_Lenti_LW279"
],
"classifications": [
"differentiated cell specimen"
],
"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) differentiated cell specimen induced to cardiac muscle cell for 12 days (cellular sub pool: subpool_LW279), male, Homo sapiens modified with CRISPRi Sp-dCas9, transduced (lentivirus) with a guide library",
"targeted_sample_term": {
"@id": "/sample-terms/CL_0000746/",
"status": "released",
"term_name": "cardiac muscle cell"
},
"taxa": "Homo sapiens"
}
],
"schema_version": "12",
"status": "preview",
"submitted_by": {
"@id": "/users/b05645f1-2d56-4a5e-b272-4601e555a3fa/",
"title": "Mpathi Nzima"
},
"submitted_files_timestamp": "2024-03-01T17:12:04.691771+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": "505f11ff-4fcd-431e-a129-c500ecf011e8"
}