{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS6756DREO/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS6756DREO",
"aliases": [
"gary-hon:CM_Pilot_2_Mini_HTO_PB_LW276"
],
"audit": {
"NOT_COMPLIANT": [
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS6756DREO](/auxiliary-sets/IGVFDS6756DREO/) has sequence file(s): [IGVFFI8741HEHC](/sequence-files/IGVFFI8741HEHC/), [IGVFFI2913YZIW](/sequence-files/IGVFFI2913YZIW/), [IGVFFI5373GJRK](/sequence-files/IGVFFI5373GJRK/), [IGVFFI6997KRUX](/sequence-files/IGVFFI6997KRUX/) which do not have any `seqspecs`. Sequence files in a file set associated with single cell data are expected to link to a sequence specification file.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_missing_seqspec",
"path": "/auxiliary-sets/IGVFDS6756DREO/"
}
]
},
"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"
},
"construct_library_sets": [
{
"@id": "/construct-library-sets/IGVFDS9629YZLO/",
"accession": "IGVFDS9629YZLO",
"file_set_type": "guide library",
"integrated_content_files": [
{
"@id": "/tabular-files/IGVFFI4543YHDW/",
"accession": "IGVFFI4543YHDW",
"content_type": "guide RNA sequences",
"status": "in progress",
"summary": "guide RNA sequences"
}
],
"status": "preview",
"summary": "guide (sgRNA) library targeting accessible genome regions in many genomic loci"
}
],
"control_for": [],
"creation_timestamp": "2024-04-25T21:44:18.555842+00:00",
"donors": [
{
"@id": "/human-donors/IGVFDO2718IDDQ/",
"accession": "IGVFDO2718IDDQ",
"aliases": [
"igvf:donor_of_H9"
],
"sex": "female",
"status": "released",
"taxa": "Homo sapiens"
}
],
"file_set_type": "cell hashing barcode sequencing",
"files": [
{
"@id": "/sequence-files/IGVFFI8741HEHC/",
"accession": "IGVFFI8741HEHC",
"aliases": [
"gary-hon:LW276C_1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-04-25T22:57:04.230270+00:00",
"file_format": "fastq",
"file_size": 304518253,
"href": "/sequence-files/IGVFFI8741HEHC/@@download/IGVFFI8741HEHC.fastq.gz",
"s3_uri": "s3://igvf-files/2024/04/25/1c65d281-1b23-44c5-8199-5e84089be939/IGVFFI8741HEHC.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//LW276C_S14_L001_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2913YZIW/",
"accession": "IGVFFI2913YZIW",
"aliases": [
"gary-hon:LW276C_1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-04-25T22:57:27.813961+00:00",
"file_format": "fastq",
"file_size": 1663005581,
"href": "/sequence-files/IGVFFI2913YZIW/@@download/IGVFFI2913YZIW.fastq.gz",
"s3_uri": "s3://igvf-files/2024/04/25/5e372cae-d1c6-49a6-8b6d-63bd1d4d5e15/IGVFFI2913YZIW.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//LW276C_S14_L001_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5373GJRK/",
"accession": "IGVFFI5373GJRK",
"aliases": [
"gary-hon:LW276C_1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-04-25T22:57:10.503711+00:00",
"file_format": "fastq",
"file_size": 307364496,
"href": "/sequence-files/IGVFFI5373GJRK/@@download/IGVFFI5373GJRK.fastq.gz",
"s3_uri": "s3://igvf-files/2024/04/25/48738752-3cd7-4743-b261-55379851f87c/IGVFFI5373GJRK.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//LW276C_S14_L001_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6997KRUX/",
"accession": "IGVFFI6997KRUX",
"aliases": [
"gary-hon:LW276C_1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-04-25T22:57:16.965905+00:00",
"file_format": "fastq",
"file_size": 842750336,
"href": "/sequence-files/IGVFFI6997KRUX/@@download/IGVFFI6997KRUX.fastq.gz",
"s3_uri": "s3://igvf-files/2024/04/25/427f9589-a4b6-4164-ab48-6f3eb328d709/IGVFFI6997KRUX.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//LW276C_S14_L001_R1_001.fastq.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS4762GRIW/"
],
"lab": {
"@id": "/labs/gary-hon/",
"title": "Gary Hon, UT"
},
"measurement_sets": [
{
"@id": "/measurement-sets/IGVFDS0307GWPA/",
"accession": "IGVFDS0307GWPA",
"aliases": [
"gary-hon:CM_Pilot_2_Mini_PB_LW276"
],
"preferred_assay_title": "Perturb-seq",
"status": "preview"
}
],
"notes": "File_set_type enum cell hashing has been renamed to be cell hashing barcode sequencing.",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM6716LOHW/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM6716LOHW",
"aliases": [
"gary-hon:differentiated_H9_shen_construct_sgRNA_PB_LW276"
],
"cellular_sub_pool": "subpool_LW276",
"classifications": [
"differentiated cell specimen"
],
"institutional_certificates": [],
"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": "Homo sapiens (female) H9 differentiated cell specimen induced to cardiac muscle cell for 12 days (cellular sub pool: subpool_LW276) modified with CRISPRi Sp-dCas9, 3 week(s) after transfection 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": "2024-04-25T22:57:04.230270+00:00",
"summary": "cell hashing barcode sequencing for CRISPR interference Perturb-seq integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"uuid": "005576ca-6a36-4410-aba8-144fc5359c91"
}