{
"@context": "/terms/",
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"AuxiliarySet",
"FileSet",
"Item"
],
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"aliases": [
"gary-hon:CM_Pilot_2_PB_sgRNA_LW231"
],
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"INTERNAL_ACTION": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS7504HTXW](/auxiliary-sets/IGVFDS7504HTXW/) has sequence file(s) [IGVFFI3844RZSE](/sequence-files/IGVFFI3844RZSE/), [IGVFFI7424BNYL](/sequence-files/IGVFFI7424BNYL/), [IGVFFI0084HLJI](/sequence-files/IGVFFI0084HLJI/), [IGVFFI2134DIIO](/sequence-files/IGVFFI2134DIIO/), [IGVFFI5003ILCS](/sequence-files/IGVFFI5003ILCS/), [IGVFFI9965OPJT](/sequence-files/IGVFFI9965OPJT/), [IGVFFI9656IWUX](/sequence-files/IGVFFI9656IWUX/), [IGVFFI2044LHZP](/sequence-files/IGVFFI2044LHZP/) 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/IGVFDS7504HTXW/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS7504HTXW](/auxiliary-sets/IGVFDS7504HTXW/) has sequence file(s): [IGVFFI3844RZSE](/sequence-files/IGVFFI3844RZSE/), [IGVFFI7424BNYL](/sequence-files/IGVFFI7424BNYL/), [IGVFFI0084HLJI](/sequence-files/IGVFFI0084HLJI/), [IGVFFI2134DIIO](/sequence-files/IGVFFI2134DIIO/), [IGVFFI5003ILCS](/sequence-files/IGVFFI5003ILCS/), [IGVFFI9965OPJT](/sequence-files/IGVFFI9965OPJT/), [IGVFFI9656IWUX](/sequence-files/IGVFFI9656IWUX/), [IGVFFI2044LHZP](/sequence-files/IGVFFI2044LHZP/) 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/IGVFDS7504HTXW/"
}
]
},
"award": {
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"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"
},
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"creation_timestamp": "2024-02-15T23:35:32.221697+00:00",
"donors": [
{
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"aliases": [
"igvf:donor_of_WTC11"
],
"sex": "male",
"status": "released",
"taxa": "Homo sapiens"
}
],
"file_set_type": "gRNA sequencing",
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{
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"accession": "IGVFFI3844RZSE",
"aliases": [
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],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-21T18:17:21.202473+00:00",
"file_format": "fastq",
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"status": "preview",
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"upload_status": "validated"
},
{
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"aliases": [
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],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-21T18:17:06.347576+00:00",
"file_format": "fastq",
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"href": "/sequence-files/IGVFFI7424BNYL/@@download/IGVFFI7424BNYL.fastq.gz",
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"sequencing_platform": "/platform-terms/EFO_0010963/",
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-03-24-McDermott-NextSeq.10X/2023-03-24/outs/fastq_path/AAC235NHV/LW231B-2_S1_L001_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0084HLJI/",
"accession": "IGVFFI0084HLJI",
"aliases": [
"gary-hon:LW231B-2_2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-21T18:17:51.383167+00:00",
"file_format": "fastq",
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"href": "/sequence-files/IGVFFI0084HLJI/@@download/IGVFFI0084HLJI.fastq.gz",
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"sequencing_platform": "/platform-terms/EFO_0010963/",
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-03-24-McDermott-NextSeq.10X/2023-03-24/outs/fastq_path/AAC235NHV/LW231B-2_S1_L002_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2134DIIO/",
"accession": "IGVFFI2134DIIO",
"aliases": [
"gary-hon:LW231B-2_2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-21T18:18:18.378979+00:00",
"file_format": "fastq",
"file_size": 1356498547,
"href": "/sequence-files/IGVFFI2134DIIO/@@download/IGVFFI2134DIIO.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/21/a2c55de7-b758-4a13-b598-022cfef719c3/IGVFFI2134DIIO.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0010963/",
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-03-24-McDermott-NextSeq.10X/2023-03-24/outs/fastq_path/AAC235NHV/LW231B-2_S1_L002_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5003ILCS/",
"accession": "IGVFFI5003ILCS",
"aliases": [
"gary-hon:LW231B-2_2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-21T18:17:58.447876+00:00",
"file_format": "fastq",
"file_size": 306108214,
"href": "/sequence-files/IGVFFI5003ILCS/@@download/IGVFFI5003ILCS.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/21/b39827f7-5144-43a3-be24-8f737c6eec0e/IGVFFI5003ILCS.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0010963/",
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-03-24-McDermott-NextSeq.10X/2023-03-24/outs/fastq_path/AAC235NHV/LW231B-2_S1_L002_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9965OPJT/",
"accession": "IGVFFI9965OPJT",
"aliases": [
"gary-hon:LW231B-2_2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-21T18:18:05.352043+00:00",
"file_format": "fastq",
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"s3_uri": "s3://igvf-files/2024/02/21/b077de65-0742-4451-819c-eeb441031008/IGVFFI9965OPJT.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0010963/",
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-03-24-McDermott-NextSeq.10X/2023-03-24/outs/fastq_path/AAC235NHV/LW231B-2_S1_L002_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9656IWUX/",
"accession": "IGVFFI9656IWUX",
"aliases": [
"gary-hon:LW231B-2_1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-21T18:17:14.294886+00:00",
"file_format": "fastq",
"file_size": 318030975,
"href": "/sequence-files/IGVFFI9656IWUX/@@download/IGVFFI9656IWUX.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/21/65156891-1d42-4e7b-a3d2-05e7318e5f04/IGVFFI9656IWUX.fastq.gz",
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"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-03-24-McDermott-NextSeq.10X/2023-03-24/outs/fastq_path/AAC235NHV/LW231B-2_S1_L001_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2044LHZP/",
"accession": "IGVFFI2044LHZP",
"aliases": [
"gary-hon:LW231B-2_1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-21T18:17:34.783226+00:00",
"file_format": "fastq",
"file_size": 1475696348,
"href": "/sequence-files/IGVFFI2044LHZP/@@download/IGVFFI2044LHZP.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/21/3439f35f-542a-4b0e-88aa-6e36c6b9f297/IGVFFI2044LHZP.fastq.gz",
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"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-03-24-McDermott-NextSeq.10X/2023-03-24/outs/fastq_path/AAC235NHV/LW231B-2_S1_L001_R2_001.fastq.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS9192YMGI/"
],
"lab": {
"@id": "/labs/gary-hon/",
"title": "Gary Hon, UT"
},
"measurement_sets": [
{
"@id": "/measurement-sets/IGVFDS1334EIHS/",
"accession": "IGVFDS1334EIHS",
"aliases": [
"gary-hon:CM_Pilot_2_PB_RNA_LW231"
],
"preferred_assay_title": "Perturb-seq",
"status": "preview"
}
],
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM7740VKXC/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM7740VKXC",
"aliases": [
"nikhil-munshi:differentited_WTC11_CM_Pilot1_PB_LW231"
],
"classifications": [
"differentiated cell specimen"
],
"construct_library_sets": [
"/construct-library-sets/IGVFDS9629YZLO/"
],
"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_LW261), male, Homo sapiens modified with CRISPRi Sp-dCas9, transfected 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": "2024-02-21T18:17:06.347576+00:00",
"summary": "gRNA sequencing for CRISPR interference Perturb-seq integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"uuid": "8bed427c-00b2-46e6-acf0-3901b32fb1eb"
}