{
"@context": "/terms/",
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"AuxiliarySet",
"FileSet",
"Item"
],
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"aliases": [
"gary-hon:CM_Pilot_2_PB_sgRNA_LW234"
],
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS2136RFQE](/auxiliary-sets/IGVFDS2136RFQE/) has sequence file(s) [IGVFFI5301SVVG](/sequence-files/IGVFFI5301SVVG/), [IGVFFI9083IKUZ](/sequence-files/IGVFFI9083IKUZ/), [IGVFFI8490GAUK](/sequence-files/IGVFFI8490GAUK/), [IGVFFI6705RMUI](/sequence-files/IGVFFI6705RMUI/), [IGVFFI2829XKCE](/sequence-files/IGVFFI2829XKCE/), [IGVFFI1008SZVT](/sequence-files/IGVFFI1008SZVT/), [IGVFFI0084VSYK](/sequence-files/IGVFFI0084VSYK/), [IGVFFI5975FQYH](/sequence-files/IGVFFI5975FQYH/) 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/IGVFDS2136RFQE/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS2136RFQE](/auxiliary-sets/IGVFDS2136RFQE/) has sequence file(s): [IGVFFI5301SVVG](/sequence-files/IGVFFI5301SVVG/), [IGVFFI9083IKUZ](/sequence-files/IGVFFI9083IKUZ/), [IGVFFI8490GAUK](/sequence-files/IGVFFI8490GAUK/), [IGVFFI6705RMUI](/sequence-files/IGVFFI6705RMUI/), [IGVFFI2829XKCE](/sequence-files/IGVFFI2829XKCE/), [IGVFFI1008SZVT](/sequence-files/IGVFFI1008SZVT/), [IGVFFI0084VSYK](/sequence-files/IGVFFI0084VSYK/), [IGVFFI5975FQYH](/sequence-files/IGVFFI5975FQYH/) 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/IGVFDS2136RFQE/"
}
]
},
"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"
},
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"creation_timestamp": "2024-02-15T23:35:39.065151+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": "IGVFFI5301SVVG",
"aliases": [
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],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-21T18:24:49.660758+00:00",
"file_format": "fastq",
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"status": "preview",
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9083IKUZ/",
"accession": "IGVFFI9083IKUZ",
"aliases": [
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],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-21T18:25:33.830845+00:00",
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"href": "/sequence-files/IGVFFI9083IKUZ/@@download/IGVFFI9083IKUZ.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/LW234B-2_S4_L002_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8490GAUK/",
"accession": "IGVFFI8490GAUK",
"aliases": [
"gary-hon:LW234B-2_1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-21T18:24:42.339197+00:00",
"file_format": "fastq",
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"href": "/sequence-files/IGVFFI8490GAUK/@@download/IGVFFI8490GAUK.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/21/30c9fba0-e7c7-4b03-a91a-8d0d155d68e3/IGVFFI8490GAUK.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/LW234B-2_S4_L001_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6705RMUI/",
"accession": "IGVFFI6705RMUI",
"aliases": [
"gary-hon:LW234B-2_2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-21T18:25:26.663669+00:00",
"file_format": "fastq",
"file_size": 347095793,
"href": "/sequence-files/IGVFFI6705RMUI/@@download/IGVFFI6705RMUI.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/21/2bffebc6-1169-43e5-95e1-085bd22dacff/IGVFFI6705RMUI.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/LW234B-2_S4_L002_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2829XKCE/",
"accession": "IGVFFI2829XKCE",
"aliases": [
"gary-hon:LW234B-2_1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-21T18:24:35.114092+00:00",
"file_format": "fastq",
"file_size": 361844130,
"href": "/sequence-files/IGVFFI2829XKCE/@@download/IGVFFI2829XKCE.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/21/83a17b29-e715-47dc-b172-b85fca9e9dab/IGVFFI2829XKCE.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/LW234B-2_S4_L001_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1008SZVT/",
"accession": "IGVFFI1008SZVT",
"aliases": [
"gary-hon:LW234B-2_1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-21T18:25:03.211315+00:00",
"file_format": "fastq",
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"s3_uri": "s3://igvf-files/2024/02/21/d7a1ecf0-6dfc-4304-90ef-7c0df2bdffd3/IGVFFI1008SZVT.fastq.gz",
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0084VSYK/",
"accession": "IGVFFI0084VSYK",
"aliases": [
"gary-hon:LW234B-2_2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-21T18:25:19.583282+00:00",
"file_format": "fastq",
"file_size": 335620018,
"href": "/sequence-files/IGVFFI0084VSYK/@@download/IGVFFI0084VSYK.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/21/996b232e-2376-4277-86ba-09b17b3a3b71/IGVFFI0084VSYK.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/LW234B-2_S4_L002_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5975FQYH/",
"accession": "IGVFFI5975FQYH",
"aliases": [
"gary-hon:LW234B-2_2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-21T18:25:46.852889+00:00",
"file_format": "fastq",
"file_size": 1317484746,
"href": "/sequence-files/IGVFFI5975FQYH/@@download/IGVFFI5975FQYH.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/21/a54c0184-f884-4f97-9c55-c2c4633f9a03/IGVFFI5975FQYH.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/LW234B-2_S4_L002_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/IGVFDS8705MRYI/",
"accession": "IGVFDS8705MRYI",
"aliases": [
"gary-hon:CM_Pilot_2_PB_RNA_LW234"
],
"preferred_assay_title": "Perturb-seq",
"status": "preview"
}
],
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM8137TZJW/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM8137TZJW",
"aliases": [
"nikhil-munshi:differentited_WTC11_CM_Pilot1_PB_LW234"
],
"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_LW264), 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": "2024-02-21T18:24:35.114092+00:00",
"summary": "gRNA sequencing for CRISPR interference Perturb-seq integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"uuid": "3568b68b-59d7-4afa-9edf-ebeddb34c283"
}