{
"@context": "/terms/",
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"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS5339UNRP",
"aliases": [
"gary-hon:TF_Perturb_Seq_Pilot_Lenti_NPC_sgRNA_LW284"
],
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS5339UNRP](/auxiliary-sets/IGVFDS5339UNRP/) has sequence file(s) [IGVFFI2235WFJR](/sequence-files/IGVFFI2235WFJR/), [IGVFFI3240FCBJ](/sequence-files/IGVFFI3240FCBJ/), [IGVFFI5213ZPGN](/sequence-files/IGVFFI5213ZPGN/), [IGVFFI7051FHND](/sequence-files/IGVFFI7051FHND/), [IGVFFI8462WRNK](/sequence-files/IGVFFI8462WRNK/), [IGVFFI1428MDRF](/sequence-files/IGVFFI1428MDRF/), [IGVFFI8576TNCS](/sequence-files/IGVFFI8576TNCS/), [IGVFFI9815IGUY](/sequence-files/IGVFFI9815IGUY/) 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/IGVFDS5339UNRP/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS5339UNRP](/auxiliary-sets/IGVFDS5339UNRP/) has sequence file(s): [IGVFFI2235WFJR](/sequence-files/IGVFFI2235WFJR/), [IGVFFI3240FCBJ](/sequence-files/IGVFFI3240FCBJ/), [IGVFFI5213ZPGN](/sequence-files/IGVFFI5213ZPGN/), [IGVFFI7051FHND](/sequence-files/IGVFFI7051FHND/), [IGVFFI8462WRNK](/sequence-files/IGVFFI8462WRNK/), [IGVFFI1428MDRF](/sequence-files/IGVFFI1428MDRF/), [IGVFFI8576TNCS](/sequence-files/IGVFFI8576TNCS/), [IGVFFI9815IGUY](/sequence-files/IGVFFI9815IGUY/) 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/IGVFDS5339UNRP/"
}
]
},
"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": "2024-02-29T16:49:45.692648+00:00",
"donors": [
{
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"accession": "IGVFDO1756PPKO",
"aliases": [
"igvf:donor_of_WTC11"
],
"sex": "male",
"status": "released",
"taxa": "Homo sapiens"
}
],
"file_set_type": "gRNA sequencing",
"files": [
{
"@id": "/sequence-files/IGVFFI2235WFJR/",
"accession": "IGVFFI2235WFJR",
"aliases": [
"gary-hon:LW284B-3_1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-01T17:24:18.297553+00:00",
"file_format": "fastq",
"file_size": 196686811,
"href": "/sequence-files/IGVFFI2235WFJR/@@download/IGVFFI2235WFJR.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/01/6bffc524-e26c-472a-b847-dc644ad8e642/IGVFFI2235WFJR.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/LW284B-3_S30_L001_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3240FCBJ/",
"accession": "IGVFFI3240FCBJ",
"aliases": [
"gary-hon:LW284B-3_1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-01T17:24:23.943777+00:00",
"file_format": "fastq",
"file_size": 511568132,
"href": "/sequence-files/IGVFFI3240FCBJ/@@download/IGVFFI3240FCBJ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/01/194064f9-308c-49cd-8ba5-b49ead4e7542/IGVFFI3240FCBJ.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/LW284B-3_S30_L001_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5213ZPGN/",
"accession": "IGVFFI5213ZPGN",
"aliases": [
"gary-hon:LW284B-3_1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-01T17:24:32.498309+00:00",
"file_format": "fastq",
"file_size": 530503031,
"href": "/sequence-files/IGVFFI5213ZPGN/@@download/IGVFFI5213ZPGN.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/01/58bd3bf4-b1b4-4544-baa4-cb2d8a7642e4/IGVFFI5213ZPGN.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/LW284B-3_S30_L001_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7051FHND/",
"accession": "IGVFFI7051FHND",
"aliases": [
"gary-hon:LW284B-3_2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-01T17:25:03.088307+00:00",
"file_format": "fastq",
"file_size": 495543128,
"href": "/sequence-files/IGVFFI7051FHND/@@download/IGVFFI7051FHND.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/01/4f2ec9ce-a6fc-413a-9d43-8b4324ebb20f/IGVFFI7051FHND.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/LW284B-3_S30_L002_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8462WRNK/",
"accession": "IGVFFI8462WRNK",
"aliases": [
"gary-hon:LW284B-3_2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-01T17:24:41.044282+00:00",
"file_format": "fastq",
"file_size": 162053922,
"href": "/sequence-files/IGVFFI8462WRNK/@@download/IGVFFI8462WRNK.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/01/ab8c0269-7397-4696-a4d9-3a25e75af909/IGVFFI8462WRNK.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/LW284B-3_S30_L002_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1428MDRF/",
"accession": "IGVFFI1428MDRF",
"aliases": [
"gary-hon:LW284B-3_2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-01T17:24:46.375732+00:00",
"file_format": "fastq",
"file_size": 184165125,
"href": "/sequence-files/IGVFFI1428MDRF/@@download/IGVFFI1428MDRF.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/01/447132ed-e319-4612-888c-65c7eb460800/IGVFFI1428MDRF.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/LW284B-3_S30_L002_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8576TNCS/",
"accession": "IGVFFI8576TNCS",
"aliases": [
"gary-hon:LW284B-3_2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-01T17:24:55.035785+00:00",
"file_format": "fastq",
"file_size": 485071070,
"href": "/sequence-files/IGVFFI8576TNCS/@@download/IGVFFI8576TNCS.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/01/89a51af2-ed1e-49c4-b258-ce5bfa8b6d72/IGVFFI8576TNCS.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/LW284B-3_S30_L002_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9815IGUY/",
"accession": "IGVFFI9815IGUY",
"aliases": [
"gary-hon:LW284B-3_1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-01T17:24:12.594077+00:00",
"file_format": "fastq",
"file_size": 173529973,
"href": "/sequence-files/IGVFFI9815IGUY/@@download/IGVFFI9815IGUY.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/01/b246c6e3-fd5c-4e6a-8ca4-fe70fa212749/IGVFFI9815IGUY.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/LW284B-3_S30_L001_I1_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/IGVFDS0657YBVN/",
"accession": "IGVFDS0657YBVN",
"aliases": [
"gary-hon:TF_Perturb_Seq_Pilot_Lenti_NPC_LW284"
],
"preferred_assay_title": "Perturb-seq",
"status": "preview"
}
],
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM2597WGYB/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM2597WGYB",
"aliases": [
"nikhil-munshi:differentited_WTC11_TF_Perturb_Seq_Pilot_NPC_Lenti_LW284"
],
"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_LW284), 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": "2024-03-01T17:24:12.594077+00:00",
"summary": "gRNA sequencing for CRISPR interference Perturb-seq integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"uuid": "e36698e3-fe43-40f7-8d16-111e73bef39b"
}