{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS8001EMIV/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS8001EMIV",
"aliases": [
"gary-hon:CM_Pilot_2_Lenti_HTO_LW266"
],
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS8001EMIV](/auxiliary-sets/IGVFDS8001EMIV/) has sequence file(s) [IGVFFI2828PDNY](/sequence-files/IGVFFI2828PDNY/), [IGVFFI9244QRVR](/sequence-files/IGVFFI9244QRVR/), [IGVFFI5054QLBL](/sequence-files/IGVFFI5054QLBL/), [IGVFFI2658YFUQ](/sequence-files/IGVFFI2658YFUQ/) 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/IGVFDS8001EMIV/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS8001EMIV](/auxiliary-sets/IGVFDS8001EMIV/) has sequence file(s): [IGVFFI2828PDNY](/sequence-files/IGVFFI2828PDNY/), [IGVFFI9244QRVR](/sequence-files/IGVFFI9244QRVR/), [IGVFFI5054QLBL](/sequence-files/IGVFFI5054QLBL/), [IGVFFI2658YFUQ](/sequence-files/IGVFFI2658YFUQ/) 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/IGVFDS8001EMIV/"
}
]
},
"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": "2024-02-15T23:35:59.689036+00:00",
"donors": [
{
"@id": "/human-donors/IGVFDO1756PPKO/",
"accession": "IGVFDO1756PPKO",
"aliases": [
"igvf:donor_of_WTC11"
],
"sex": "male",
"status": "released",
"taxa": "Homo sapiens"
}
],
"file_set_type": "cell hashing barcode sequencing",
"files": [
{
"@id": "/sequence-files/IGVFFI2828PDNY/",
"accession": "IGVFFI2828PDNY",
"aliases": [
"gary-hon:LW266C_1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-20T20:39:39.363387+00:00",
"file_format": "fastq",
"file_size": 114340979,
"href": "/sequence-files/IGVFFI2828PDNY/@@download/IGVFFI2828PDNY.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/20/58a22053-24aa-4eca-a8ec-4593906dfeb4/IGVFFI2828PDNY.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/LW266C_S14_L001_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9244QRVR/",
"accession": "IGVFFI9244QRVR",
"aliases": [
"gary-hon:LW266C_1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-20T20:39:44.623752+00:00",
"file_format": "fastq",
"file_size": 162533207,
"href": "/sequence-files/IGVFFI9244QRVR/@@download/IGVFFI9244QRVR.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/20/c9908c67-c0b1-441f-adfb-f1596669d8ee/IGVFFI9244QRVR.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/LW266C_S14_L001_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5054QLBL/",
"accession": "IGVFFI5054QLBL",
"aliases": [
"gary-hon:LW266C_1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-20T20:39:57.200142+00:00",
"file_format": "fastq",
"file_size": 967905168,
"href": "/sequence-files/IGVFFI5054QLBL/@@download/IGVFFI5054QLBL.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/20/e931f9b4-556a-4c5d-9ff2-6b54d4a56c44/IGVFFI5054QLBL.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/LW266C_S14_L001_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2658YFUQ/",
"accession": "IGVFFI2658YFUQ",
"aliases": [
"gary-hon:LW266C_1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-20T20:39:49.999067+00:00",
"file_format": "fastq",
"file_size": 366747527,
"href": "/sequence-files/IGVFFI2658YFUQ/@@download/IGVFFI2658YFUQ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/20/30457521-eca1-42d1-9634-28c0463f8d33/IGVFFI2658YFUQ.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/LW266C_S14_L001_R1_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/IGVFDS5931MYJN/",
"accession": "IGVFDS5931MYJN",
"aliases": [
"gary-hon:CM_Pilot_2_Lenti_RNA_LW266"
],
"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/IGVFSM4930FDUF/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM4930FDUF",
"aliases": [
"nikhil-munshi:differentited_WTC11_CM_Pilot1_Lenti_LW266"
],
"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_LW266), 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": "2024-02-20T20:39:39.363387+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": "c257f9d7-dc7b-4eff-924c-9010b83ec38e"
}