{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS1349DIMY/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS1349DIMY",
"aliases": [
"gary-hon:CM_Pilot_2_Lenti_sgRNA_LW263"
],
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS1349DIMY](/auxiliary-sets/IGVFDS1349DIMY/) has sequence file(s) [IGVFFI5886EXSK](/sequence-files/IGVFFI5886EXSK/), [IGVFFI5666YZNA](/sequence-files/IGVFFI5666YZNA/), [IGVFFI4467KSXD](/sequence-files/IGVFFI4467KSXD/), [IGVFFI0207DWDS](/sequence-files/IGVFFI0207DWDS/) 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/IGVFDS1349DIMY/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS1349DIMY](/auxiliary-sets/IGVFDS1349DIMY/) has sequence file(s): [IGVFFI5886EXSK](/sequence-files/IGVFFI5886EXSK/), [IGVFFI5666YZNA](/sequence-files/IGVFFI5666YZNA/), [IGVFFI4467KSXD](/sequence-files/IGVFFI4467KSXD/), [IGVFFI0207DWDS](/sequence-files/IGVFFI0207DWDS/) 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/IGVFDS1349DIMY/"
}
]
},
"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": "2024-02-15T23:35:53.995213+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/IGVFFI5886EXSK/",
"accession": "IGVFFI5886EXSK",
"aliases": [
"gary-hon:LW263B_1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-20T20:35:36.046908+00:00",
"file_format": "fastq",
"file_size": 264457331,
"href": "/sequence-files/IGVFFI5886EXSK/@@download/IGVFFI5886EXSK.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/20/4b2beb8a-567f-4d83-868b-37ef048f4ab7/IGVFFI5886EXSK.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/LW263B_S3_L001_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5666YZNA/",
"accession": "IGVFFI5666YZNA",
"aliases": [
"gary-hon:LW263B_1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-20T20:35:29.047718+00:00",
"file_format": "fastq",
"file_size": 288856630,
"href": "/sequence-files/IGVFFI5666YZNA/@@download/IGVFFI5666YZNA.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/20/915c184f-5f08-4d55-9df3-bd00adf8838e/IGVFFI5666YZNA.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/LW263B_S3_L001_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4467KSXD/",
"accession": "IGVFFI4467KSXD",
"aliases": [
"gary-hon:LW263B_1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-20T20:35:42.838584+00:00",
"file_format": "fastq",
"file_size": 871800777,
"href": "/sequence-files/IGVFFI4467KSXD/@@download/IGVFFI4467KSXD.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/20/94bcc67b-c436-4ae7-bf24-9fbc275fcebe/IGVFFI4467KSXD.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/LW263B_S3_L001_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0207DWDS/",
"accession": "IGVFFI0207DWDS",
"aliases": [
"gary-hon:LW263B_1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-20T20:35:54.405082+00:00",
"file_format": "fastq",
"file_size": 1450778343,
"href": "/sequence-files/IGVFFI0207DWDS/@@download/IGVFFI0207DWDS.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/20/e34073f6-6ee3-4f46-88ee-77ed3aaa85d3/IGVFFI0207DWDS.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/LW263B_S3_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/IGVFDS4965SLDK/",
"accession": "IGVFDS4965SLDK",
"aliases": [
"gary-hon:CM_Pilot_2_Lenti_RNA_LW263"
],
"preferred_assay_title": "Perturb-seq",
"status": "preview"
}
],
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM0333RWYR/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM0333RWYR",
"aliases": [
"nikhil-munshi:differentited_WTC11_CM_Pilot1_Lenti_LW263"
],
"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_LW263), 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": "2024-02-20T20:35:29.047718+00:00",
"summary": "gRNA sequencing for CRISPR interference Perturb-seq integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"uuid": "af6be6e3-5bda-4758-8717-db09722b9830"
}