{
"@context": "/terms/",
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"FileSet",
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],
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],
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{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS2536BETY](/auxiliary-sets/IGVFDS2536BETY/) has sequence file(s): [IGVFFI5824TPXK](/sequence-files/IGVFFI5824TPXK/), [IGVFFI5824GVQO](/sequence-files/IGVFFI5824GVQO/), [IGVFFI9466GZAJ](/sequence-files/IGVFFI9466GZAJ/), [IGVFFI7907JKFW](/sequence-files/IGVFFI7907JKFW/) which do not have any `seqspecs`. Sequence files in a file set associated with single cell data are expected to link to a sequence specification file.",
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"name": "audit_missing_seqspec",
"path": "/auxiliary-sets/IGVFDS2536BETY/"
}
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"component": "functional characterization",
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"title": "Gary Hon"
},
"title": "Multiscale functional characterization of genomic variation in human developmental disorders"
},
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{
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"accession": "IGVFDS0346MQBH",
"file_set_type": "guide library",
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{
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"accession": "IGVFFI9879UTKX",
"content_type": "guide RNA sequences",
"status": "in progress",
"summary": "guide RNA sequences"
}
],
"status": "preview",
"summary": "guide (sgRNA) library targeting accessible genome regions in many genomic loci"
}
],
"control_for": [],
"creation_timestamp": "2024-08-16T20:05:07.881114+00:00",
"data_use_limitation_summaries": [
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],
"donors": [
{
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"accession": "IGVFDO1756PPKO",
"aliases": [
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],
"sex": "male",
"status": "released",
"taxa": "Homo sapiens"
}
],
"file_set_type": "gRNA sequencing",
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{
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"accession": "IGVFFI5824TPXK",
"aliases": [
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],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-01-14T21:33:59.434783+00:00",
"file_format": "fastq",
"file_size": 598718623,
"href": "/sequence-files/IGVFFI5824TPXK/@@download/IGVFFI5824TPXK.fastq.gz",
"md5sum": "4c31f5b9ba6cd1350e31b1f78a3b8daa",
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5824GVQO/",
"accession": "IGVFFI5824GVQO",
"aliases": [
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],
"content_type": "reads",
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"creation_timestamp": "2025-01-14T21:34:30.361091+00:00",
"file_format": "fastq",
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"status": "preview",
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9466GZAJ/",
"accession": "IGVFFI9466GZAJ",
"aliases": [
"gary-hon:LW428B_6_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-01-14T21:35:24.452278+00:00",
"file_format": "fastq",
"file_size": 5267677224,
"href": "/sequence-files/IGVFFI9466GZAJ/@@download/IGVFFI9466GZAJ.fastq.gz",
"md5sum": "13e2b9e199e7a89d750f3e083c057d5d",
"s3_uri": "s3://igvf-files/2025/01/14/750e132b-e17c-466f-8098-1f5893d06f5d/IGVFFI9466GZAJ.fastq.gz",
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"status": "preview",
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7907JKFW/",
"accession": "IGVFFI7907JKFW",
"aliases": [
"gary-hon:LW428B_6_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-01-14T21:34:15.650416+00:00",
"file_format": "fastq",
"file_size": 612333412,
"href": "/sequence-files/IGVFFI7907JKFW/@@download/IGVFFI7907JKFW.fastq.gz",
"md5sum": "07f830fcaefc200ae6bc067a11d4cafe",
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"sequencing_platform": "/platform-terms/EFO_0022841/",
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2024/2024-05-01-Novogene-NovaSeq.Hon19_20/sgRNA//LW428B_S14_L006_I2_001.fastq.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS5498SDRJ/"
],
"lab": {
"@id": "/labs/gary-hon/",
"title": "Gary Hon, UT"
},
"measurement_sets": [
{
"@id": "/measurement-sets/IGVFDS4629NPBV/",
"accession": "IGVFDS4629NPBV",
"aliases": [
"gary-hon:differentited_WTC11_CM_Pilot2_Mini_LPv4_LW428"
],
"preferred_assay_title": "Perturb-seq",
"status": "preview"
}
],
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM9285BBSI/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM9285BBSI",
"aliases": [
"nikhil-munshi:differentited_WTC11_CM_Pilot2_Mini_LPv4_LW428"
],
"cellular_sub_pool": "subpool_LW428",
"classifications": [
"differentiated cell specimen"
],
"institutional_certificates": [],
"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": "Homo sapiens (male) GM25256 (WTC-11) differentiated cell specimen induced to cardiac muscle cell for 12 days (cellular sub pool: subpool_LW428) modified with CRISPRi Sp-dCas9, transduced (lentivirus) with a guide library",
"targeted_sample_term": {
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"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": "2025-01-14T21:33:59.434783+00:00",
"summary": "gRNA sequencing for CRISPR interference Perturb-seq integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"uuid": "1543ac52-27dd-4e50-a19e-cce401a7e84d"
}