{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS6787YPNQ/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS6787YPNQ",
"aliases": [
"gary-hon:CM_Pilot_2_Lenti_sgRNA_LW267"
],
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS6787YPNQ](/auxiliary-sets/IGVFDS6787YPNQ/) has sequence file(s) [IGVFFI7677YUQR](/sequence-files/IGVFFI7677YUQR/), [IGVFFI9760OIHQ](/sequence-files/IGVFFI9760OIHQ/), [IGVFFI3213XORW](/sequence-files/IGVFFI3213XORW/), [IGVFFI7835NCQX](/sequence-files/IGVFFI7835NCQX/) 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/IGVFDS6787YPNQ/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS6787YPNQ](/auxiliary-sets/IGVFDS6787YPNQ/) has sequence file(s): [IGVFFI7677YUQR](/sequence-files/IGVFFI7677YUQR/), [IGVFFI9760OIHQ](/sequence-files/IGVFFI9760OIHQ/), [IGVFFI3213XORW](/sequence-files/IGVFFI3213XORW/), [IGVFFI7835NCQX](/sequence-files/IGVFFI7835NCQX/) 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/IGVFDS6787YPNQ/"
}
]
},
"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": "2024-02-15T23:36:02.669622+00:00",
"donors": [
{
"@id": "/human-donors/IGVFDO1756PPKO/",
"accession": "IGVFDO1756PPKO",
"aliases": [
"igvf:donor_of_WTC11"
],
"sex": "male",
"status": "released",
"taxa": "Homo sapiens"
}
],
"file_set_type": "gRNA sequencing",
"files": [
{
"@id": "/sequence-files/IGVFFI7677YUQR/",
"accession": "IGVFFI7677YUQR",
"aliases": [
"gary-hon:LW267B_1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-20T20:40:09.598456+00:00",
"file_format": "fastq",
"file_size": 240464425,
"href": "/sequence-files/IGVFFI7677YUQR/@@download/IGVFFI7677YUQR.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/20/e4bea2d1-9cb0-4d67-bbeb-b73d03968575/IGVFFI7677YUQR.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0010963/",
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-07-07-McDermott-NextSeq.10X.run1.sgRNA_HTO/2023-07-07/outs/fastq_path/AACV7CFM5/LW267B_S7_L001_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9760OIHQ/",
"accession": "IGVFFI9760OIHQ",
"aliases": [
"gary-hon:LW267B_1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-20T20:40:15.616256+00:00",
"file_format": "fastq",
"file_size": 263698472,
"href": "/sequence-files/IGVFFI9760OIHQ/@@download/IGVFFI9760OIHQ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/20/1cf5b9d6-ea6b-4fd0-a375-fd1c45a99279/IGVFFI9760OIHQ.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0010963/",
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-07-07-McDermott-NextSeq.10X.run1.sgRNA_HTO/2023-07-07/outs/fastq_path/AACV7CFM5/LW267B_S7_L001_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3213XORW/",
"accession": "IGVFFI3213XORW",
"aliases": [
"gary-hon:LW267B_1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-20T20:40:21.812244+00:00",
"file_format": "fastq",
"file_size": 811343256,
"href": "/sequence-files/IGVFFI3213XORW/@@download/IGVFFI3213XORW.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/20/95b7ff07-97b2-40fc-a6ed-99e78aca0b43/IGVFFI3213XORW.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0010963/",
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-07-07-McDermott-NextSeq.10X.run1.sgRNA_HTO/2023-07-07/outs/fastq_path/AACV7CFM5/LW267B_S7_L001_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7835NCQX/",
"accession": "IGVFFI7835NCQX",
"aliases": [
"gary-hon:LW267B_1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-20T20:40:32.873379+00:00",
"file_format": "fastq",
"file_size": 1330463815,
"href": "/sequence-files/IGVFFI7835NCQX/@@download/IGVFFI7835NCQX.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/20/23ab9ac5-c1fc-4eaa-826d-c237a51c5b55/IGVFFI7835NCQX.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0010963/",
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-07-07-McDermott-NextSeq.10X.run1.sgRNA_HTO/2023-07-07/outs/fastq_path/AACV7CFM5/LW267B_S7_L001_R2_001.fastq.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS4003HZAB/"
],
"lab": {
"@id": "/labs/gary-hon/",
"title": "Gary Hon, UT"
},
"measurement_sets": [
{
"@id": "/measurement-sets/IGVFDS4088YJYC/",
"accession": "IGVFDS4088YJYC",
"aliases": [
"gary-hon:CM_Pilot_2_Lenti_RNA_LW267"
],
"preferred_assay_title": "Perturb-seq",
"status": "preview"
}
],
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM5628VVVG/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM5628VVVG",
"aliases": [
"nikhil-munshi:differentited_WTC11_CM_Pilot1_Lenti_LW267"
],
"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_LW267), male, 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": "2024-02-20T20:40:09.598456+00:00",
"summary": "gRNA sequencing for CRISPR interference Perturb-seq integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"uuid": "25bce165-5ca8-4db2-8b48-d4ea25f813dc"
}