{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS7986GKWR/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS7986GKWR",
"aliases": [
"gary-hon:TF_Perturb_Seq_Pilot_Lenti_NPC_sgRNA_LW282"
],
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS7986GKWR](/auxiliary-sets/IGVFDS7986GKWR/) has sequence file(s) [IGVFFI9536AHMJ](/sequence-files/IGVFFI9536AHMJ/), [IGVFFI2700GHXT](/sequence-files/IGVFFI2700GHXT/), [IGVFFI9141KKTA](/sequence-files/IGVFFI9141KKTA/), [IGVFFI3164PDJY](/sequence-files/IGVFFI3164PDJY/), [IGVFFI3852EJBS](/sequence-files/IGVFFI3852EJBS/), [IGVFFI3491WALI](/sequence-files/IGVFFI3491WALI/), [IGVFFI2014MVWI](/sequence-files/IGVFFI2014MVWI/), [IGVFFI3418CTXX](/sequence-files/IGVFFI3418CTXX/) 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/IGVFDS7986GKWR/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS7986GKWR](/auxiliary-sets/IGVFDS7986GKWR/) has sequence file(s): [IGVFFI9536AHMJ](/sequence-files/IGVFFI9536AHMJ/), [IGVFFI2700GHXT](/sequence-files/IGVFFI2700GHXT/), [IGVFFI9141KKTA](/sequence-files/IGVFFI9141KKTA/), [IGVFFI3164PDJY](/sequence-files/IGVFFI3164PDJY/), [IGVFFI3852EJBS](/sequence-files/IGVFFI3852EJBS/), [IGVFFI3491WALI](/sequence-files/IGVFFI3491WALI/), [IGVFFI2014MVWI](/sequence-files/IGVFFI2014MVWI/), [IGVFFI3418CTXX](/sequence-files/IGVFFI3418CTXX/) 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/IGVFDS7986GKWR/"
}
]
},
"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": "2024-02-29T16:49:41.114169+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/IGVFFI9536AHMJ/",
"accession": "IGVFFI9536AHMJ",
"aliases": [
"gary-hon:LW282B-3_1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-01T17:18:57.994472+00:00",
"file_format": "fastq",
"file_size": 577319014,
"href": "/sequence-files/IGVFFI9536AHMJ/@@download/IGVFFI9536AHMJ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/01/242593fd-a10d-41be-8a8a-5731a5bc0ca0/IGVFFI9536AHMJ.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/LW282B-3_S28_L001_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2700GHXT/",
"accession": "IGVFFI2700GHXT",
"aliases": [
"gary-hon:LW282B-3_2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-01T17:19:15.763482+00:00",
"file_format": "fastq",
"file_size": 167168334,
"href": "/sequence-files/IGVFFI2700GHXT/@@download/IGVFFI2700GHXT.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/01/dea00f85-1980-41b8-a379-a62cd8b22706/IGVFFI2700GHXT.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/LW282B-3_S28_L002_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9141KKTA/",
"accession": "IGVFFI9141KKTA",
"aliases": [
"gary-hon:LW282B-3_2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-01T17:19:20.938768+00:00",
"file_format": "fastq",
"file_size": 190649709,
"href": "/sequence-files/IGVFFI9141KKTA/@@download/IGVFFI9141KKTA.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/01/23773240-57ce-4ec8-88ca-9c4627c9369d/IGVFFI9141KKTA.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/LW282B-3_S28_L002_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3164PDJY/",
"accession": "IGVFFI3164PDJY",
"aliases": [
"gary-hon:LW282B-3_2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-01T17:19:31.083240+00:00",
"file_format": "fastq",
"file_size": 548240665,
"href": "/sequence-files/IGVFFI3164PDJY/@@download/IGVFFI3164PDJY.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/01/37c9c69b-27f7-4dbd-ab41-0c665be07fff/IGVFFI3164PDJY.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/LW282B-3_S28_L002_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3852EJBS/",
"accession": "IGVFFI3852EJBS",
"aliases": [
"gary-hon:LW282B-3_1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-01T17:18:46.886742+00:00",
"file_format": "fastq",
"file_size": 181364173,
"href": "/sequence-files/IGVFFI3852EJBS/@@download/IGVFFI3852EJBS.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/01/cd9c5736-f833-4d1e-a5b6-b84d674e48d4/IGVFFI3852EJBS.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/LW282B-3_S28_L001_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3491WALI/",
"accession": "IGVFFI3491WALI",
"aliases": [
"gary-hon:LW282B-3_1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-01T17:18:52.470899+00:00",
"file_format": "fastq",
"file_size": 202487793,
"href": "/sequence-files/IGVFFI3491WALI/@@download/IGVFFI3491WALI.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/01/1e563912-dae6-433c-a7eb-b2145a9485ed/IGVFFI3491WALI.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/LW282B-3_S28_L001_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2014MVWI/",
"accession": "IGVFFI2014MVWI",
"aliases": [
"gary-hon:LW282B-3_1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-01T17:19:06.818534+00:00",
"file_format": "fastq",
"file_size": 595695995,
"href": "/sequence-files/IGVFFI2014MVWI/@@download/IGVFFI2014MVWI.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/01/9c97b259-5727-4c8d-b150-cf3875a13fe0/IGVFFI2014MVWI.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/LW282B-3_S28_L001_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3418CTXX/",
"accession": "IGVFFI3418CTXX",
"aliases": [
"gary-hon:LW282B-3_2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-01T17:19:39.556202+00:00",
"file_format": "fastq",
"file_size": 557960420,
"href": "/sequence-files/IGVFFI3418CTXX/@@download/IGVFFI3418CTXX.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/01/a3326444-a5a3-491b-8e4c-ce3cf91bb3ce/IGVFFI3418CTXX.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/LW282B-3_S28_L002_R2_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"
}
],
"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": "2024-03-01T17:18:46.886742+00:00",
"summary": "gRNA sequencing for CRISPR interference Perturb-seq integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"uuid": "d5a68106-23e3-4c77-a051-ea01f760e0db"
}