{
"@context": "/terms/",
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"FileSet",
"Item"
],
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"aliases": [
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],
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{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS4210TUPX](/auxiliary-sets/IGVFDS4210TUPX/) has sequence file(s): [IGVFFI6877UQHQ](/sequence-files/IGVFFI6877UQHQ/), [IGVFFI8174NAEK](/sequence-files/IGVFFI8174NAEK/), [IGVFFI8554AKFO](/sequence-files/IGVFFI8554AKFO/), [IGVFFI2887DIIX](/sequence-files/IGVFFI2887DIIX/) 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.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_missing_seqspec",
"path": "/auxiliary-sets/IGVFDS4210TUPX/"
}
]
},
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"component": "functional characterization",
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"@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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{
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"accession": "IGVFDS0346MQBH",
"file_set_type": "guide library",
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{
"@id": "/tabular-files/IGVFFI9879UTKX/",
"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": "2024-08-16T20:05:11.345678+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": "cell hashing barcode sequencing",
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{
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"accession": "IGVFFI6877UQHQ",
"aliases": [
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],
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"creation_timestamp": "2025-01-14T21:29:41.252065+00:00",
"file_format": "fastq",
"file_size": 409285332,
"href": "/sequence-files/IGVFFI6877UQHQ/@@download/IGVFFI6877UQHQ.fastq.gz",
"md5sum": "bece9daf41b9f3a62f0ed4774f228bd3",
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8174NAEK/",
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],
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"creation_timestamp": "2025-01-14T21:29:55.221346+00:00",
"file_format": "fastq",
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8554AKFO/",
"accession": "IGVFFI8554AKFO",
"aliases": [
"gary-hon:LW429C_6_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-01-14T21:30:09.840720+00:00",
"file_format": "fastq",
"file_size": 3631443116,
"href": "/sequence-files/IGVFFI8554AKFO/@@download/IGVFFI8554AKFO.fastq.gz",
"md5sum": "d079adfbfe40b4b9fbcf8a97f50aa427",
"s3_uri": "s3://igvf-files/2025/01/14/7b6b8944-d953-4e44-97cd-d1eaf8bd385f/IGVFFI8554AKFO.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0022841/",
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2887DIIX/",
"accession": "IGVFFI2887DIIX",
"aliases": [
"gary-hon:LW429C_6_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-01-14T21:30:50.278392+00:00",
"file_format": "fastq",
"file_size": 3780287119,
"href": "/sequence-files/IGVFFI2887DIIX/@@download/IGVFFI2887DIIX.fastq.gz",
"md5sum": "3d49ec9c947f4a0ee1904446b7021124",
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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/HTO//LW429C_S23_L006_R2_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/IGVFDS3695BOGD/",
"accession": "IGVFDS3695BOGD",
"aliases": [
"gary-hon:differentited_WTC11_CM_Pilot2_Mini_LPv4_LW429"
],
"preferred_assay_title": "Perturb-seq",
"status": "preview"
}
],
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM7766HOYF/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM7766HOYF",
"aliases": [
"nikhil-munshi:differentited_WTC11_CM_Pilot2_Mini_LPv4_LW429"
],
"cellular_sub_pool": "subpool_LW429",
"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_LW429) modified with CRISPRi Sp-dCas9, transduced (lentivirus) 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": "2025-01-14T21:29:41.252065+00:00",
"summary": "cell hashing barcode sequencing for CRISPR interference Perturb-seq integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"uuid": "cc055442-206f-444e-97f6-673367a29671"
}