{
"@context": "/terms/",
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"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS8202GWXE",
"aliases": [
"gary-hon:CM_Pilot_2_PB_sgRNA_LW232"
],
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS8202GWXE](/auxiliary-sets/IGVFDS8202GWXE/) has sequence file(s) [IGVFFI3533OPFH](/sequence-files/IGVFFI3533OPFH/), [IGVFFI4177QZAY](/sequence-files/IGVFFI4177QZAY/), [IGVFFI5494QEZY](/sequence-files/IGVFFI5494QEZY/), [IGVFFI0174OYDP](/sequence-files/IGVFFI0174OYDP/), [IGVFFI2826DJRC](/sequence-files/IGVFFI2826DJRC/), [IGVFFI8476XMZO](/sequence-files/IGVFFI8476XMZO/), [IGVFFI3449QVQP](/sequence-files/IGVFFI3449QVQP/), [IGVFFI5474JBFR](/sequence-files/IGVFFI5474JBFR/) 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/IGVFDS8202GWXE/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS8202GWXE](/auxiliary-sets/IGVFDS8202GWXE/) has sequence file(s): [IGVFFI3533OPFH](/sequence-files/IGVFFI3533OPFH/), [IGVFFI4177QZAY](/sequence-files/IGVFFI4177QZAY/), [IGVFFI5494QEZY](/sequence-files/IGVFFI5494QEZY/), [IGVFFI0174OYDP](/sequence-files/IGVFFI0174OYDP/), [IGVFFI2826DJRC](/sequence-files/IGVFFI2826DJRC/), [IGVFFI8476XMZO](/sequence-files/IGVFFI8476XMZO/), [IGVFFI3449QVQP](/sequence-files/IGVFFI3449QVQP/), [IGVFFI5474JBFR](/sequence-files/IGVFFI5474JBFR/) 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/IGVFDS8202GWXE/"
}
]
},
"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": "2024-02-15T23:35:34.440721+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": [
{
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"accession": "IGVFFI3533OPFH",
"aliases": [
"gary-hon:LW232B-2_2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-21T18:20:22.099293+00:00",
"file_format": "fastq",
"file_size": 269871798,
"href": "/sequence-files/IGVFFI3533OPFH/@@download/IGVFFI3533OPFH.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/21/87a5b7a3-a993-41c1-a3f6-46a6c981fd0e/IGVFFI3533OPFH.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/LW232B-2_S2_L002_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4177QZAY/",
"accession": "IGVFFI4177QZAY",
"aliases": [
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],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-21T18:20:28.358464+00:00",
"file_format": "fastq",
"file_size": 350757112,
"href": "/sequence-files/IGVFFI4177QZAY/@@download/IGVFFI4177QZAY.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/21/5f49e0b6-f52f-41fc-9710-85f988d2160f/IGVFFI4177QZAY.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/LW232B-2_S2_L002_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5494QEZY/",
"accession": "IGVFFI5494QEZY",
"aliases": [
"gary-hon:LW232B-2_2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-21T18:20:35.307647+00:00",
"file_format": "fastq",
"file_size": 984899686,
"href": "/sequence-files/IGVFFI5494QEZY/@@download/IGVFFI5494QEZY.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/21/2abf8f5f-8504-44e5-bf8c-ba0095829035/IGVFFI5494QEZY.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/LW232B-2_S2_L002_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0174OYDP/",
"accession": "IGVFFI0174OYDP",
"aliases": [
"gary-hon:LW232B-2_1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-21T18:19:52.770679+00:00",
"file_format": "fastq",
"file_size": 1037910193,
"href": "/sequence-files/IGVFFI0174OYDP/@@download/IGVFFI0174OYDP.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/21/5673f507-9396-4c6d-b1d5-14b4913c299a/IGVFFI0174OYDP.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/LW232B-2_S2_L001_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2826DJRC/",
"accession": "IGVFFI2826DJRC",
"aliases": [
"gary-hon:LW232B-2_1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-21T18:20:06.532481+00:00",
"file_format": "fastq",
"file_size": 1341767161,
"href": "/sequence-files/IGVFFI2826DJRC/@@download/IGVFFI2826DJRC.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/21/63eff765-2eae-45af-acaf-5834926a8845/IGVFFI2826DJRC.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/LW232B-2_S2_L001_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8476XMZO/",
"accession": "IGVFFI8476XMZO",
"aliases": [
"gary-hon:LW232B-2_1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-21T18:19:38.935555+00:00",
"file_format": "fastq",
"file_size": 299467880,
"href": "/sequence-files/IGVFFI8476XMZO/@@download/IGVFFI8476XMZO.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/21/2e0ad324-5f3b-4ecc-9c33-1f232902d608/IGVFFI8476XMZO.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/LW232B-2_S2_L001_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3449QVQP/",
"accession": "IGVFFI3449QVQP",
"aliases": [
"gary-hon:LW232B-2_1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-21T18:19:45.530428+00:00",
"file_format": "fastq",
"file_size": 370048067,
"href": "/sequence-files/IGVFFI3449QVQP/@@download/IGVFFI3449QVQP.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/21/aeed36ef-e4de-452b-9c5d-ab04480473f4/IGVFFI3449QVQP.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/LW232B-2_S2_L001_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5474JBFR/",
"accession": "IGVFFI5474JBFR",
"aliases": [
"gary-hon:LW232B-2_2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-21T18:20:47.865643+00:00",
"file_format": "fastq",
"file_size": 1265375217,
"href": "/sequence-files/IGVFFI5474JBFR/@@download/IGVFFI5474JBFR.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/21/e9d76c84-c9bc-45d2-aa07-4c3a0f705514/IGVFFI5474JBFR.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/LW232B-2_S2_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/IGVFDS9005AVSB/",
"accession": "IGVFDS9005AVSB",
"aliases": [
"gary-hon:CM_Pilot_2_PB_RNA_LW232"
],
"preferred_assay_title": "Perturb-seq",
"status": "preview"
}
],
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM4953FLXN/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM4953FLXN",
"aliases": [
"nikhil-munshi:differentited_WTC11_CM_Pilot1_PB_LW232"
],
"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_LW262), 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": "2024-02-21T18:19:38.935555+00:00",
"summary": "gRNA sequencing for CRISPR interference Perturb-seq integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"uuid": "69a89c7a-e5ef-4848-b6b4-64451f40dfdb"
}