{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS4510VNEU/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS4510VNEU",
"aliases": [
"gary-hon:CM_Pilot_2_Mini_sgRNA_PB_LW276"
],
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS4510VNEU](/auxiliary-sets/IGVFDS4510VNEU/) has sequence file(s) [IGVFFI4591SIBG](/sequence-files/IGVFFI4591SIBG/), [IGVFFI9879ZPBO](/sequence-files/IGVFFI9879ZPBO/), [IGVFFI2118VBKO](/sequence-files/IGVFFI2118VBKO/), [IGVFFI3883TQKS](/sequence-files/IGVFFI3883TQKS/) 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/IGVFDS4510VNEU/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS4510VNEU](/auxiliary-sets/IGVFDS4510VNEU/) has sequence file(s): [IGVFFI4591SIBG](/sequence-files/IGVFFI4591SIBG/), [IGVFFI9879ZPBO](/sequence-files/IGVFFI9879ZPBO/), [IGVFFI2118VBKO](/sequence-files/IGVFFI2118VBKO/), [IGVFFI3883TQKS](/sequence-files/IGVFFI3883TQKS/) 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/IGVFDS4510VNEU/"
}
]
},
"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": "2024-04-25T21:44:17.703174+00:00",
"donors": [
{
"@id": "/human-donors/IGVFDO2718IDDQ/",
"accession": "IGVFDO2718IDDQ",
"aliases": [
"igvf:donor_of_H9"
],
"sex": "female",
"status": "released",
"taxa": "Homo sapiens"
}
],
"file_set_type": "gRNA sequencing",
"files": [
{
"@id": "/sequence-files/IGVFFI4591SIBG/",
"accession": "IGVFFI4591SIBG",
"aliases": [
"gary-hon:LW276B_1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-04-25T23:00:22.860433+00:00",
"file_format": "fastq",
"file_size": 251725418,
"href": "/sequence-files/IGVFFI4591SIBG/@@download/IGVFFI4591SIBG.fastq.gz",
"s3_uri": "s3://igvf-files/2024/04/25/d1c03a14-ad54-4e2c-979b-8f0872f799cb/IGVFFI4591SIBG.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0010963/",
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-09-11-McDermott-NextSeq.10X/2023-09-11/outs/fastq_path/AACYY52M5//LW276B_S16_L001_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9879ZPBO/",
"accession": "IGVFFI9879ZPBO",
"aliases": [
"gary-hon:LW276B_1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-04-25T23:00:17.116678+00:00",
"file_format": "fastq",
"file_size": 215441893,
"href": "/sequence-files/IGVFFI9879ZPBO/@@download/IGVFFI9879ZPBO.fastq.gz",
"s3_uri": "s3://igvf-files/2024/04/25/458adea2-5dfd-4b0d-822f-66cd4bd2e7b6/IGVFFI9879ZPBO.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0010963/",
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-09-11-McDermott-NextSeq.10X/2023-09-11/outs/fastq_path/AACYY52M5//LW276B_S16_L001_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2118VBKO/",
"accession": "IGVFFI2118VBKO",
"aliases": [
"gary-hon:LW276B_1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-04-25T23:00:28.825954+00:00",
"file_format": "fastq",
"file_size": 681580079,
"href": "/sequence-files/IGVFFI2118VBKO/@@download/IGVFFI2118VBKO.fastq.gz",
"s3_uri": "s3://igvf-files/2024/04/25/0dfa2ba2-fb5b-4601-915d-4f563f8f436e/IGVFFI2118VBKO.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0010963/",
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-09-11-McDermott-NextSeq.10X/2023-09-11/outs/fastq_path/AACYY52M5//LW276B_S16_L001_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3883TQKS/",
"accession": "IGVFFI3883TQKS",
"aliases": [
"gary-hon:LW276B_1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-04-25T23:00:38.725085+00:00",
"file_format": "fastq",
"file_size": 1166065399,
"href": "/sequence-files/IGVFFI3883TQKS/@@download/IGVFFI3883TQKS.fastq.gz",
"s3_uri": "s3://igvf-files/2024/04/25/d2fbd2d9-3d51-4667-9c4e-9888b6636a32/IGVFFI3883TQKS.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0010963/",
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-09-11-McDermott-NextSeq.10X/2023-09-11/outs/fastq_path/AACYY52M5//LW276B_S16_L001_R2_001.fastq.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS4762GRIW/"
],
"lab": {
"@id": "/labs/gary-hon/",
"title": "Gary Hon, UT"
},
"measurement_sets": [
{
"@id": "/measurement-sets/IGVFDS0307GWPA/",
"accession": "IGVFDS0307GWPA",
"aliases": [
"gary-hon:CM_Pilot_2_Mini_PB_LW276"
],
"preferred_assay_title": "Perturb-seq",
"status": "preview"
}
],
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM6716LOHW/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM6716LOHW",
"aliases": [
"gary-hon:differentiated_H9_shen_construct_sgRNA_PB_LW276"
],
"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_0003045/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"aliases": [
"igvf:H9"
],
"status": "released",
"summary": "H9",
"term_name": "H9"
}
],
"status": "preview",
"summary": "H9 differentiated cell specimen induced to cardiac muscle cell for 12 days (cellular sub pool: subpool_LW276), female, 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": "2024-04-25T23:00:17.116678+00:00",
"summary": "gRNA sequencing for CRISPR interference Perturb-seq integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"uuid": "e396641e-5e78-491c-bd7d-831346d1773a"
}