{
"@context": "/terms/",
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"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS4262EBDF",
"aliases": [
"gary-hon:TF_Perturb_Seq_Pilot_Lenti_NPC_sgRNA_LW283"
],
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS4262EBDF](/auxiliary-sets/IGVFDS4262EBDF/) has sequence file(s) [IGVFFI1665CADL](/sequence-files/IGVFFI1665CADL/), [IGVFFI3519VNMQ](/sequence-files/IGVFFI3519VNMQ/), [IGVFFI2060GRST](/sequence-files/IGVFFI2060GRST/), [IGVFFI8010OOFR](/sequence-files/IGVFFI8010OOFR/), [IGVFFI9758LRXH](/sequence-files/IGVFFI9758LRXH/), [IGVFFI6625XXQD](/sequence-files/IGVFFI6625XXQD/), [IGVFFI1976NIRG](/sequence-files/IGVFFI1976NIRG/), [IGVFFI1491BIMR](/sequence-files/IGVFFI1491BIMR/) 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/IGVFDS4262EBDF/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS4262EBDF](/auxiliary-sets/IGVFDS4262EBDF/) has sequence file(s): [IGVFFI1665CADL](/sequence-files/IGVFFI1665CADL/), [IGVFFI3519VNMQ](/sequence-files/IGVFFI3519VNMQ/), [IGVFFI2060GRST](/sequence-files/IGVFFI2060GRST/), [IGVFFI8010OOFR](/sequence-files/IGVFFI8010OOFR/), [IGVFFI9758LRXH](/sequence-files/IGVFFI9758LRXH/), [IGVFFI6625XXQD](/sequence-files/IGVFFI6625XXQD/), [IGVFFI1976NIRG](/sequence-files/IGVFFI1976NIRG/), [IGVFFI1491BIMR](/sequence-files/IGVFFI1491BIMR/) 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/IGVFDS4262EBDF/"
}
]
},
"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": "2024-02-29T16:49:43.565223+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": [
{
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"accession": "IGVFFI1665CADL",
"aliases": [
"gary-hon:LW283B-3_1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-01T17:21:44.098772+00:00",
"file_format": "fastq",
"file_size": 208578277,
"href": "/sequence-files/IGVFFI1665CADL/@@download/IGVFFI1665CADL.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/01/2d5ed479-154e-4dda-8e1c-02a1e8c11e5c/IGVFFI1665CADL.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/LW283B-3_S29_L001_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3519VNMQ/",
"accession": "IGVFFI3519VNMQ",
"aliases": [
"gary-hon:LW283B-3_2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-01T17:22:20.429635+00:00",
"file_format": "fastq",
"file_size": 561064454,
"href": "/sequence-files/IGVFFI3519VNMQ/@@download/IGVFFI3519VNMQ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/01/8fb1284e-81cc-44fe-98d9-8859b9049bbb/IGVFFI3519VNMQ.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/LW283B-3_S29_L002_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2060GRST/",
"accession": "IGVFFI2060GRST",
"aliases": [
"gary-hon:LW283B-3_1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-01T17:21:38.396125+00:00",
"file_format": "fastq",
"file_size": 210628860,
"href": "/sequence-files/IGVFFI2060GRST/@@download/IGVFFI2060GRST.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/01/d1379e90-1f4d-449e-8042-2c32b42de5a6/IGVFFI2060GRST.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/LW283B-3_S29_L001_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8010OOFR/",
"accession": "IGVFFI8010OOFR",
"aliases": [
"gary-hon:LW283B-3_1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-01T17:22:00.275103+00:00",
"file_format": "fastq",
"file_size": 634195130,
"href": "/sequence-files/IGVFFI8010OOFR/@@download/IGVFFI8010OOFR.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/01/ecc1137b-b176-4c30-a472-a008497b23f7/IGVFFI8010OOFR.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/LW283B-3_S29_L001_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9758LRXH/",
"accession": "IGVFFI9758LRXH",
"aliases": [
"gary-hon:LW283B-3_2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-01T17:22:09.366212+00:00",
"file_format": "fastq",
"file_size": 190782618,
"href": "/sequence-files/IGVFFI9758LRXH/@@download/IGVFFI9758LRXH.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/01/1cb03e63-9104-44e9-bd38-81b3cfb9b0d6/IGVFFI9758LRXH.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/LW283B-3_S29_L002_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6625XXQD/",
"accession": "IGVFFI6625XXQD",
"aliases": [
"gary-hon:LW283B-3_2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-01T17:22:29.106457+00:00",
"file_format": "fastq",
"file_size": 575844907,
"href": "/sequence-files/IGVFFI6625XXQD/@@download/IGVFFI6625XXQD.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/01/8e683f19-cfd0-4ec2-a6bb-ddd94bcf18d1/IGVFFI6625XXQD.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/LW283B-3_S29_L002_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1976NIRG/",
"accession": "IGVFFI1976NIRG",
"aliases": [
"gary-hon:LW283B-3_1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-01T17:21:49.771418+00:00",
"file_format": "fastq",
"file_size": 609498759,
"href": "/sequence-files/IGVFFI1976NIRG/@@download/IGVFFI1976NIRG.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/01/a070c17b-73b4-4928-9a96-020046b22578/IGVFFI1976NIRG.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/LW283B-3_S29_L001_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1491BIMR/",
"accession": "IGVFFI1491BIMR",
"aliases": [
"gary-hon:LW283B-3_2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-01T17:22:14.962675+00:00",
"file_format": "fastq",
"file_size": 195020187,
"href": "/sequence-files/IGVFFI1491BIMR/@@download/IGVFFI1491BIMR.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/01/64f34e4b-cb4a-4429-935c-58d6a6a98f98/IGVFFI1491BIMR.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/LW283B-3_S29_L002_I2_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/IGVFDS4028IRAH/",
"accession": "IGVFDS4028IRAH",
"aliases": [
"gary-hon:TF_Perturb_Seq_Pilot_Lenti_NPC_LW283"
],
"preferred_assay_title": "Perturb-seq",
"status": "preview"
}
],
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM8464JMJS/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM8464JMJS",
"aliases": [
"nikhil-munshi:differentited_WTC11_TF_Perturb_Seq_Pilot_NPC_Lenti_LW283"
],
"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_LW283), 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": "2024-03-01T17:21:38.396125+00:00",
"summary": "gRNA sequencing for CRISPR interference Perturb-seq integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"uuid": "f3917bb6-5094-49bc-ab07-cb8f10778ec0"
}