{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS8726ORVQ/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS8726ORVQ",
"aliases": [
"gary-hon:CM_Pilot_2_Mini_sgRNA_Lenti_LW272"
],
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS8726ORVQ](/auxiliary-sets/IGVFDS8726ORVQ/) has sequence file(s) [IGVFFI9255ZWLL](/sequence-files/IGVFFI9255ZWLL/), [IGVFFI9316DTIE](/sequence-files/IGVFFI9316DTIE/), [IGVFFI0045RQHO](/sequence-files/IGVFFI0045RQHO/), [IGVFFI8537ABID](/sequence-files/IGVFFI8537ABID/) 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/IGVFDS8726ORVQ/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS8726ORVQ](/auxiliary-sets/IGVFDS8726ORVQ/) has sequence file(s): [IGVFFI9255ZWLL](/sequence-files/IGVFFI9255ZWLL/), [IGVFFI9316DTIE](/sequence-files/IGVFFI9316DTIE/), [IGVFFI0045RQHO](/sequence-files/IGVFFI0045RQHO/), [IGVFFI8537ABID](/sequence-files/IGVFFI8537ABID/) 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/IGVFDS8726ORVQ/"
}
]
},
"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": "2024-04-25T21:44:11.651388+00:00",
"donors": [
{
"@id": "/human-donors/IGVFDO2718IDDQ/",
"accession": "IGVFDO2718IDDQ",
"aliases": [
"igvf:donor_of_H9"
],
"sex": "female",
"status": "released",
"taxa": "Homo sapiens"
}
],
"file_set_type": "gRNA sequencing",
"files": [
{
"@id": "/sequence-files/IGVFFI9255ZWLL/",
"accession": "IGVFFI9255ZWLL",
"aliases": [
"gary-hon:LW272B_1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-04-25T22:54:28.551086+00:00",
"file_format": "fastq",
"file_size": 169965302,
"href": "/sequence-files/IGVFFI9255ZWLL/@@download/IGVFFI9255ZWLL.fastq.gz",
"s3_uri": "s3://igvf-files/2024/04/25/87d7c50f-cb28-4ec9-88c3-37cf56b5fbcc/IGVFFI9255ZWLL.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//LW272B_S10_L001_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9316DTIE/",
"accession": "IGVFFI9316DTIE",
"aliases": [
"gary-hon:LW272B_1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-04-25T22:54:34.111281+00:00",
"file_format": "fastq",
"file_size": 590356560,
"href": "/sequence-files/IGVFFI9316DTIE/@@download/IGVFFI9316DTIE.fastq.gz",
"s3_uri": "s3://igvf-files/2024/04/25/e0110788-82ba-4869-bb8c-997f76a979d9/IGVFFI9316DTIE.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//LW272B_S10_L001_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0045RQHO/",
"accession": "IGVFFI0045RQHO",
"aliases": [
"gary-hon:LW272B_1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-04-25T22:54:42.951435+00:00",
"file_format": "fastq",
"file_size": 667995131,
"href": "/sequence-files/IGVFFI0045RQHO/@@download/IGVFFI0045RQHO.fastq.gz",
"s3_uri": "s3://igvf-files/2024/04/25/0940977d-bbf4-4109-a72b-5c4282570354/IGVFFI0045RQHO.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//LW272B_S10_L001_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8537ABID/",
"accession": "IGVFFI8537ABID",
"aliases": [
"gary-hon:LW272B_1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-04-25T22:54:22.809374+00:00",
"file_format": "fastq",
"file_size": 205171813,
"href": "/sequence-files/IGVFFI8537ABID/@@download/IGVFFI8537ABID.fastq.gz",
"s3_uri": "s3://igvf-files/2024/04/25/b4dfad5d-3019-475b-8e2f-a34d0fbfd7d6/IGVFFI8537ABID.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//LW272B_S10_L001_I1_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"
}
],
"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": "2024-04-25T22:54:22.809374+00:00",
"summary": "gRNA sequencing for CRISPR interference Perturb-seq integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"uuid": "3b9d2eb9-21ff-4f9d-84a9-2be64f7a0625"
}