{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS5031XGGB/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS5031XGGB",
"aliases": [
"gary-hon:CM_Pilot_2_Lenti_sgRNA_LW268"
],
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS5031XGGB](/auxiliary-sets/IGVFDS5031XGGB/) has sequence file(s) [IGVFFI5384GZHX](/sequence-files/IGVFFI5384GZHX/), [IGVFFI3916MOXA](/sequence-files/IGVFFI3916MOXA/), [IGVFFI2756EFLJ](/sequence-files/IGVFFI2756EFLJ/), [IGVFFI3594VEZZ](/sequence-files/IGVFFI3594VEZZ/) 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/IGVFDS5031XGGB/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS5031XGGB](/auxiliary-sets/IGVFDS5031XGGB/) has sequence file(s): [IGVFFI5384GZHX](/sequence-files/IGVFFI5384GZHX/), [IGVFFI3916MOXA](/sequence-files/IGVFFI3916MOXA/), [IGVFFI2756EFLJ](/sequence-files/IGVFFI2756EFLJ/), [IGVFFI3594VEZZ](/sequence-files/IGVFFI3594VEZZ/) 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/IGVFDS5031XGGB/"
}
]
},
"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": "2024-02-15T23:36:07.759078+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/IGVFFI5384GZHX/",
"accession": "IGVFFI5384GZHX",
"aliases": [
"gary-hon:LW268B_1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-20T20:41:17.907052+00:00",
"file_format": "fastq",
"file_size": 296598355,
"href": "/sequence-files/IGVFFI5384GZHX/@@download/IGVFFI5384GZHX.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/20/8547738b-afd0-4c8c-a99d-8ed67e2ad621/IGVFFI5384GZHX.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/LW268B_S8_L001_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3916MOXA/",
"accession": "IGVFFI3916MOXA",
"aliases": [
"gary-hon:LW268B_1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-20T20:41:28.315745+00:00",
"file_format": "fastq",
"file_size": 270476419,
"href": "/sequence-files/IGVFFI3916MOXA/@@download/IGVFFI3916MOXA.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/20/f81a1552-8ca5-488c-87f7-1dec97c45881/IGVFFI3916MOXA.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/LW268B_S8_L001_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2756EFLJ/",
"accession": "IGVFFI2756EFLJ",
"aliases": [
"gary-hon:LW268B_1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-20T20:41:39.588465+00:00",
"file_format": "fastq",
"file_size": 757436825,
"href": "/sequence-files/IGVFFI2756EFLJ/@@download/IGVFFI2756EFLJ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/20/ffcb351b-23c5-4528-a7f8-c926969456d0/IGVFFI2756EFLJ.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/LW268B_S8_L001_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3594VEZZ/",
"accession": "IGVFFI3594VEZZ",
"aliases": [
"gary-hon:LW268B_1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-20T20:41:50.156838+00:00",
"file_format": "fastq",
"file_size": 1259125164,
"href": "/sequence-files/IGVFFI3594VEZZ/@@download/IGVFFI3594VEZZ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/20/ec10a6f8-1f7b-493f-8d9f-f9799061e59c/IGVFFI3594VEZZ.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/LW268B_S8_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/IGVFDS5173WYKU/",
"accession": "IGVFDS5173WYKU",
"aliases": [
"gary-hon:CM_Pilot_2_Lenti_RNA_LW268"
],
"preferred_assay_title": "Perturb-seq",
"status": "preview"
}
],
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM2215YBLM/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM2215YBLM",
"aliases": [
"nikhil-munshi:differentited_WTC11_CM_Pilot1_Lenti_LW268"
],
"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_LW268), 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": "2024-02-20T20:41:17.907052+00:00",
"summary": "gRNA sequencing for CRISPR interference Perturb-seq integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"uuid": "bc67f0e3-50dd-48b5-b074-48a44978df41"
}