{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS3533NRTW/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS3533NRTW",
"aliases": [
"gary-hon:CM_Pilot_2_Lenti_sgRNA_LW264"
],
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS3533NRTW](/auxiliary-sets/IGVFDS3533NRTW/) has sequence file(s) [IGVFFI2147OLQC](/sequence-files/IGVFFI2147OLQC/), [IGVFFI8172KHSP](/sequence-files/IGVFFI8172KHSP/), [IGVFFI9339EFZQ](/sequence-files/IGVFFI9339EFZQ/), [IGVFFI2974UJYR](/sequence-files/IGVFFI2974UJYR/) 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/IGVFDS3533NRTW/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS3533NRTW](/auxiliary-sets/IGVFDS3533NRTW/) has sequence file(s): [IGVFFI2147OLQC](/sequence-files/IGVFFI2147OLQC/), [IGVFFI8172KHSP](/sequence-files/IGVFFI8172KHSP/), [IGVFFI9339EFZQ](/sequence-files/IGVFFI9339EFZQ/), [IGVFFI2974UJYR](/sequence-files/IGVFFI2974UJYR/) 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/IGVFDS3533NRTW/"
}
]
},
"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": "2024-02-15T23:35:56.416456+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/IGVFFI2147OLQC/",
"accession": "IGVFFI2147OLQC",
"aliases": [
"gary-hon:LW264B_1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-20T20:37:07.621500+00:00",
"file_format": "fastq",
"file_size": 1467673336,
"href": "/sequence-files/IGVFFI2147OLQC/@@download/IGVFFI2147OLQC.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/20/f08b6f37-1a93-4264-abe8-534be7b3c324/IGVFFI2147OLQC.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/LW264B_S4_L001_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8172KHSP/",
"accession": "IGVFFI8172KHSP",
"aliases": [
"gary-hon:LW264B_1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-20T20:36:55.850232+00:00",
"file_format": "fastq",
"file_size": 877201922,
"href": "/sequence-files/IGVFFI8172KHSP/@@download/IGVFFI8172KHSP.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/20/7b9db749-e6c4-4c3d-a90a-72178eafba87/IGVFFI8172KHSP.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/LW264B_S4_L001_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9339EFZQ/",
"accession": "IGVFFI9339EFZQ",
"aliases": [
"gary-hon:LW264B_1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-20T20:36:38.823366+00:00",
"file_format": "fastq",
"file_size": 256182511,
"href": "/sequence-files/IGVFFI9339EFZQ/@@download/IGVFFI9339EFZQ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/20/58c40bff-8c8f-4959-8035-029b2a1d11dc/IGVFFI9339EFZQ.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/LW264B_S4_L001_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2974UJYR/",
"accession": "IGVFFI2974UJYR",
"aliases": [
"gary-hon:LW264B_1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-20T20:36:49.284672+00:00",
"file_format": "fastq",
"file_size": 288192620,
"href": "/sequence-files/IGVFFI2974UJYR/@@download/IGVFFI2974UJYR.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/20/64368b53-6cb6-4377-b9d5-b05ae0f5ce8a/IGVFFI2974UJYR.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/LW264B_S4_L001_I2_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/IGVFDS6054GEKL/",
"accession": "IGVFDS6054GEKL",
"aliases": [
"gary-hon:CM_Pilot_2_Lenti_RNA_LW264"
],
"preferred_assay_title": "Perturb-seq",
"status": "preview"
}
],
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM0981UTUA/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM0981UTUA",
"aliases": [
"nikhil-munshi:differentited_WTC11_CM_Pilot1_Lenti_LW264"
],
"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_LW264), 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": "2024-02-20T20:36:38.823366+00:00",
"summary": "gRNA sequencing for CRISPR interference Perturb-seq integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"uuid": "d9821d5d-a782-43dd-8cde-dcd99664f862"
}