{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS3567LQMB/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS3567LQMB",
"aliases": [
"gary-hon:TF_Perturb_Seq_Pilot_Lenti_NPC_HTO_LW282"
],
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS3567LQMB](/auxiliary-sets/IGVFDS3567LQMB/) has sequence file(s) [IGVFFI1692PBQW](/sequence-files/IGVFFI1692PBQW/), [IGVFFI5482BVUW](/sequence-files/IGVFFI5482BVUW/), [IGVFFI9298IPBX](/sequence-files/IGVFFI9298IPBX/), [IGVFFI0409KOWK](/sequence-files/IGVFFI0409KOWK/), [IGVFFI3785WYDT](/sequence-files/IGVFFI3785WYDT/), [IGVFFI5436EVPV](/sequence-files/IGVFFI5436EVPV/), [IGVFFI2912RLLI](/sequence-files/IGVFFI2912RLLI/), [IGVFFI4099YBZW](/sequence-files/IGVFFI4099YBZW/) 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/IGVFDS3567LQMB/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS3567LQMB](/auxiliary-sets/IGVFDS3567LQMB/) has sequence file(s): [IGVFFI1692PBQW](/sequence-files/IGVFFI1692PBQW/), [IGVFFI5482BVUW](/sequence-files/IGVFFI5482BVUW/), [IGVFFI9298IPBX](/sequence-files/IGVFFI9298IPBX/), [IGVFFI0409KOWK](/sequence-files/IGVFFI0409KOWK/), [IGVFFI3785WYDT](/sequence-files/IGVFFI3785WYDT/), [IGVFFI5436EVPV](/sequence-files/IGVFFI5436EVPV/), [IGVFFI2912RLLI](/sequence-files/IGVFFI2912RLLI/), [IGVFFI4099YBZW](/sequence-files/IGVFFI4099YBZW/) 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/IGVFDS3567LQMB/"
}
]
},
"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": "2024-02-29T16:49:42.163081+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/IGVFFI1692PBQW/",
"accession": "IGVFFI1692PBQW",
"aliases": [
"gary-hon:LW282C_2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-01T17:20:24.853473+00:00",
"file_format": "fastq",
"file_size": 393349835,
"href": "/sequence-files/IGVFFI1692PBQW/@@download/IGVFFI1692PBQW.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/01/34371965-fc0f-460f-9ac2-28d751756a27/IGVFFI1692PBQW.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/LW282C_S6_L002_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5482BVUW/",
"accession": "IGVFFI5482BVUW",
"aliases": [
"gary-hon:LW282C_1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-01T17:19:48.002089+00:00",
"file_format": "fastq",
"file_size": 90462073,
"href": "/sequence-files/IGVFFI5482BVUW/@@download/IGVFFI5482BVUW.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/01/ff7eefbf-9b3e-4484-baba-8591dd7d2e37/IGVFFI5482BVUW.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/LW282C_S6_L001_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9298IPBX/",
"accession": "IGVFFI9298IPBX",
"aliases": [
"gary-hon:LW282C_1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-01T17:19:57.274288+00:00",
"file_format": "fastq",
"file_size": 206346812,
"href": "/sequence-files/IGVFFI9298IPBX/@@download/IGVFFI9298IPBX.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/01/2dc1bcfd-dbff-4206-af56-bdfa9fbd7e28/IGVFFI9298IPBX.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/LW282C_S6_L001_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0409KOWK/",
"accession": "IGVFFI0409KOWK",
"aliases": [
"gary-hon:LW282C_1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-01T17:20:02.908423+00:00",
"file_format": "fastq",
"file_size": 423929610,
"href": "/sequence-files/IGVFFI0409KOWK/@@download/IGVFFI0409KOWK.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/01/b11daee1-d1bc-4ce0-913e-476bf0c5deff/IGVFFI0409KOWK.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/LW282C_S6_L001_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3785WYDT/",
"accession": "IGVFFI3785WYDT",
"aliases": [
"gary-hon:LW282C_2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-01T17:20:10.246303+00:00",
"file_format": "fastq",
"file_size": 84289667,
"href": "/sequence-files/IGVFFI3785WYDT/@@download/IGVFFI3785WYDT.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/01/aab3fbc0-d849-4238-ae8b-46ccec1aa85f/IGVFFI3785WYDT.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/LW282C_S6_L002_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5436EVPV/",
"accession": "IGVFFI5436EVPV",
"aliases": [
"gary-hon:LW282C_2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-01T17:20:14.781715+00:00",
"file_format": "fastq",
"file_size": 85770859,
"href": "/sequence-files/IGVFFI5436EVPV/@@download/IGVFFI5436EVPV.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/01/ab0c232c-5a85-485b-b87b-f034a4e8211a/IGVFFI5436EVPV.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/LW282C_S6_L002_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2912RLLI/",
"accession": "IGVFFI2912RLLI",
"aliases": [
"gary-hon:LW282C_1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-01T17:19:52.656142+00:00",
"file_format": "fastq",
"file_size": 91193292,
"href": "/sequence-files/IGVFFI2912RLLI/@@download/IGVFFI2912RLLI.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/01/fdfe24d8-3b66-4a26-8d3b-ee01d493e126/IGVFFI2912RLLI.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/LW282C_S6_L001_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4099YBZW/",
"accession": "IGVFFI4099YBZW",
"aliases": [
"gary-hon:LW282C_2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-01T17:20:19.178355+00:00",
"file_format": "fastq",
"file_size": 192242176,
"href": "/sequence-files/IGVFFI4099YBZW/@@download/IGVFFI4099YBZW.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/01/a451df1d-70bd-4b71-ada8-25ecc3fe8b5e/IGVFFI4099YBZW.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/LW282C_S6_L002_R1_001.fastq.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS1588TVKF/"
],
"lab": {
"@id": "/labs/gary-hon/",
"title": "Gary Hon, UT"
},
"measurement_sets": [
{
"@id": "/measurement-sets/IGVFDS8810ABUD/",
"accession": "IGVFDS8810ABUD",
"aliases": [
"gary-hon:TF_Perturb_Seq_Pilot_Lenti_NPC_LW282"
],
"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/IGVFSM1288TQKF/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM1288TQKF",
"aliases": [
"nikhil-munshi:differentited_WTC11_TF_Perturb_Seq_Pilot_NPC_Lenti_LW282"
],
"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 neural stem cell for 20 days (cellular sub pool: subpool_LW282), male, Homo sapiens modified with CRISPRi Sp-dCas9, transduced (lentivirus) with a guide library",
"targeted_sample_term": {
"@id": "/sample-terms/CL_0000047/",
"status": "preview",
"term_name": "neural stem cell"
},
"taxa": "Homo sapiens"
}
],
"schema_version": "12",
"status": "preview",
"submitted_by": {
"@id": "/users/b05645f1-2d56-4a5e-b272-4601e555a3fa/",
"title": "Mpathi Nzima"
},
"submitted_files_timestamp": "2024-03-01T17:19:48.002089+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": "61960601-2019-48b6-98b6-5e516b4285b4"
}