{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS8839RSIR/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS8839RSIR",
"aliases": [
"gary-hon:CM_Pilot_2_Mini_HTO_Lenti_LW272"
],
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS8839RSIR](/auxiliary-sets/IGVFDS8839RSIR/) has sequence file(s) [IGVFFI3688WTIX](/sequence-files/IGVFFI3688WTIX/), [IGVFFI0982WORL](/sequence-files/IGVFFI0982WORL/), [IGVFFI9175HBPO](/sequence-files/IGVFFI9175HBPO/), [IGVFFI8689DYXM](/sequence-files/IGVFFI8689DYXM/) 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/IGVFDS8839RSIR/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS8839RSIR](/auxiliary-sets/IGVFDS8839RSIR/) has sequence file(s): [IGVFFI3688WTIX](/sequence-files/IGVFFI3688WTIX/), [IGVFFI0982WORL](/sequence-files/IGVFFI0982WORL/), [IGVFFI9175HBPO](/sequence-files/IGVFFI9175HBPO/), [IGVFFI8689DYXM](/sequence-files/IGVFFI8689DYXM/) 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/IGVFDS8839RSIR/"
}
]
},
"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": "2024-04-25T21:44:12.237845+00:00",
"donors": [
{
"@id": "/human-donors/IGVFDO2718IDDQ/",
"accession": "IGVFDO2718IDDQ",
"aliases": [
"igvf:donor_of_H9"
],
"sex": "female",
"status": "released",
"taxa": "Homo sapiens"
}
],
"file_set_type": "cell hashing barcode sequencing",
"files": [
{
"@id": "/sequence-files/IGVFFI3688WTIX/",
"accession": "IGVFFI3688WTIX",
"aliases": [
"gary-hon:LW272C_1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-04-25T22:54:54.144713+00:00",
"file_format": "fastq",
"file_size": 354800486,
"href": "/sequence-files/IGVFFI3688WTIX/@@download/IGVFFI3688WTIX.fastq.gz",
"s3_uri": "s3://igvf-files/2024/04/25/c6614d92-2b8c-47bc-9a73-6715226852f2/IGVFFI3688WTIX.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0010963/",
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-12-22-McDermott-NextSeq.10X/2023-12-22/outs/fastq_path/AAF5CKNM5//LW272C_S6_L001_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0982WORL/",
"accession": "IGVFFI0982WORL",
"aliases": [
"gary-hon:LW272C_1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-04-25T22:55:07.998241+00:00",
"file_format": "fastq",
"file_size": 1027749505,
"href": "/sequence-files/IGVFFI0982WORL/@@download/IGVFFI0982WORL.fastq.gz",
"s3_uri": "s3://igvf-files/2024/04/25/b1d91161-bdf1-4307-9611-5aed3e1bb360/IGVFFI0982WORL.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0010963/",
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-12-22-McDermott-NextSeq.10X/2023-12-22/outs/fastq_path/AAF5CKNM5//LW272C_S6_L001_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9175HBPO/",
"accession": "IGVFFI9175HBPO",
"aliases": [
"gary-hon:LW272C_1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-04-25T22:55:01.040896+00:00",
"file_format": "fastq",
"file_size": 350554708,
"href": "/sequence-files/IGVFFI9175HBPO/@@download/IGVFFI9175HBPO.fastq.gz",
"s3_uri": "s3://igvf-files/2024/04/25/1cb5c1a0-fcc5-4829-a34b-029f231e334c/IGVFFI9175HBPO.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0010963/",
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-12-22-McDermott-NextSeq.10X/2023-12-22/outs/fastq_path/AAF5CKNM5//LW272C_S6_L001_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8689DYXM/",
"accession": "IGVFFI8689DYXM",
"aliases": [
"gary-hon:LW272C_1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-04-25T22:55:20.876367+00:00",
"file_format": "fastq",
"file_size": 2014478635,
"href": "/sequence-files/IGVFFI8689DYXM/@@download/IGVFFI8689DYXM.fastq.gz",
"s3_uri": "s3://igvf-files/2024/04/25/9e815cc4-2928-459c-8a5c-0cbb6da98649/IGVFFI8689DYXM.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0010963/",
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-12-22-McDermott-NextSeq.10X/2023-12-22/outs/fastq_path/AAF5CKNM5//LW272C_S6_L001_R2_001.fastq.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS2873EPIU/"
],
"lab": {
"@id": "/labs/gary-hon/",
"title": "Gary Hon, UT"
},
"measurement_sets": [
{
"@id": "/measurement-sets/IGVFDS4940ELQK/",
"accession": "IGVFDS4940ELQK",
"aliases": [
"gary-hon:CM_Pilot_2_Mini_Lenti_LW272"
],
"preferred_assay_title": "Perturb-seq",
"status": "preview"
}
],
"notes": "File_set_type enum cell hashing has been renamed to be cell hashing barcode sequencing.",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM1608DJBB/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM1608DJBB",
"aliases": [
"gary-hon:differentiated_H9_shen_construct_sgRNA_Lenti_LW272"
],
"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_LW272), female, Homo sapiens 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": "2024-04-25T22:54:54.144713+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": "d520cd40-3bbe-4a23-bd2f-cb1e5c3667dc"
}