{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS6402AFPQ/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS6402AFPQ",
"aliases": [
"gary-hon:CM_Pilot_2_PB_HTO_LW238"
],
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS6402AFPQ](/auxiliary-sets/IGVFDS6402AFPQ/) has sequence file(s) [IGVFFI7732YRYL](/sequence-files/IGVFFI7732YRYL/), [IGVFFI3342AZOL](/sequence-files/IGVFFI3342AZOL/), [IGVFFI2001BUVU](/sequence-files/IGVFFI2001BUVU/), [IGVFFI2156WUHQ](/sequence-files/IGVFFI2156WUHQ/), [IGVFFI2591CCVN](/sequence-files/IGVFFI2591CCVN/), [IGVFFI8893RYFI](/sequence-files/IGVFFI8893RYFI/), [IGVFFI1306YVIM](/sequence-files/IGVFFI1306YVIM/), [IGVFFI0841DIBZ](/sequence-files/IGVFFI0841DIBZ/) 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/IGVFDS6402AFPQ/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS6402AFPQ](/auxiliary-sets/IGVFDS6402AFPQ/) has sequence file(s): [IGVFFI7732YRYL](/sequence-files/IGVFFI7732YRYL/), [IGVFFI3342AZOL](/sequence-files/IGVFFI3342AZOL/), [IGVFFI2001BUVU](/sequence-files/IGVFFI2001BUVU/), [IGVFFI2156WUHQ](/sequence-files/IGVFFI2156WUHQ/), [IGVFFI2591CCVN](/sequence-files/IGVFFI2591CCVN/), [IGVFFI8893RYFI](/sequence-files/IGVFFI8893RYFI/), [IGVFFI1306YVIM](/sequence-files/IGVFFI1306YVIM/), [IGVFFI0841DIBZ](/sequence-files/IGVFFI0841DIBZ/) 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/IGVFDS6402AFPQ/"
}
]
},
"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": "2024-02-15T23:35:47.236973+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/IGVFFI7732YRYL/",
"accession": "IGVFFI7732YRYL",
"aliases": [
"gary-hon:LW238C_1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-21T18:36:03.707575+00:00",
"file_format": "fastq",
"file_size": 371738756,
"href": "/sequence-files/IGVFFI7732YRYL/@@download/IGVFFI7732YRYL.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/21/b766200b-2c34-4e89-ad65-93c5ba7f2147/IGVFFI7732YRYL.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0010963/",
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-03-24-McDermott-NextSeq.10X/2023-03-24/outs/fastq_path/AAC235NHV/LW238C_S16_L001_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3342AZOL/",
"accession": "IGVFFI3342AZOL",
"aliases": [
"gary-hon:LW238C_1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-21T18:35:58.224519+00:00",
"file_format": "fastq",
"file_size": 118846104,
"href": "/sequence-files/IGVFFI3342AZOL/@@download/IGVFFI3342AZOL.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/21/2c3f0770-9b14-4f46-a289-d1fa81307338/IGVFFI3342AZOL.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0010963/",
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-03-24-McDermott-NextSeq.10X/2023-03-24/outs/fastq_path/AAC235NHV/LW238C_S16_L001_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2001BUVU/",
"accession": "IGVFFI2001BUVU",
"aliases": [
"gary-hon:LW238C_1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-21T18:35:52.524926+00:00",
"file_format": "fastq",
"file_size": 124052158,
"href": "/sequence-files/IGVFFI2001BUVU/@@download/IGVFFI2001BUVU.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/21/af78def0-d44a-4788-ae1f-3aa28ca0e99e/IGVFFI2001BUVU.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0010963/",
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-03-24-McDermott-NextSeq.10X/2023-03-24/outs/fastq_path/AAC235NHV/LW238C_S16_L001_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2156WUHQ/",
"accession": "IGVFFI2156WUHQ",
"aliases": [
"gary-hon:LW238C_2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-21T18:36:42.682162+00:00",
"file_format": "fastq",
"file_size": 634276805,
"href": "/sequence-files/IGVFFI2156WUHQ/@@download/IGVFFI2156WUHQ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/21/a3babf0c-cddd-451c-a0aa-2b2fe8812fa0/IGVFFI2156WUHQ.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0010963/",
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-03-24-McDermott-NextSeq.10X/2023-03-24/outs/fastq_path/AAC235NHV/LW238C_S16_L002_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2591CCVN/",
"accession": "IGVFFI2591CCVN",
"aliases": [
"gary-hon:LW238C_2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-21T18:36:31.187563+00:00",
"file_format": "fastq",
"file_size": 341476697,
"href": "/sequence-files/IGVFFI2591CCVN/@@download/IGVFFI2591CCVN.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/21/aa13d9fe-4680-491b-97bb-eeccaf86f264/IGVFFI2591CCVN.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0010963/",
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-03-24-McDermott-NextSeq.10X/2023-03-24/outs/fastq_path/AAC235NHV/LW238C_S16_L002_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8893RYFI/",
"accession": "IGVFFI8893RYFI",
"aliases": [
"gary-hon:LW238C_1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-21T18:36:11.048842+00:00",
"file_format": "fastq",
"file_size": 694617881,
"href": "/sequence-files/IGVFFI8893RYFI/@@download/IGVFFI8893RYFI.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/21/b723934b-2174-45bd-8754-60b2fd44d914/IGVFFI8893RYFI.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0010963/",
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-03-24-McDermott-NextSeq.10X/2023-03-24/outs/fastq_path/AAC235NHV/LW238C_S16_L001_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1306YVIM/",
"accession": "IGVFFI1306YVIM",
"aliases": [
"gary-hon:LW238C_2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-21T18:36:21.084029+00:00",
"file_format": "fastq",
"file_size": 113058373,
"href": "/sequence-files/IGVFFI1306YVIM/@@download/IGVFFI1306YVIM.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/21/b8e133a3-b482-4932-b3ea-8b7caa26d4aa/IGVFFI1306YVIM.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0010963/",
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-03-24-McDermott-NextSeq.10X/2023-03-24/outs/fastq_path/AAC235NHV/LW238C_S16_L002_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0841DIBZ/",
"accession": "IGVFFI0841DIBZ",
"aliases": [
"gary-hon:LW238C_2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-21T18:36:26.205902+00:00",
"file_format": "fastq",
"file_size": 108884732,
"href": "/sequence-files/IGVFFI0841DIBZ/@@download/IGVFFI0841DIBZ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/21/50dca050-c511-45d4-942d-7a699028e280/IGVFFI0841DIBZ.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0010963/",
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-03-24-McDermott-NextSeq.10X/2023-03-24/outs/fastq_path/AAC235NHV/LW238C_S16_L002_I2_001.fastq.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS9192YMGI/"
],
"lab": {
"@id": "/labs/gary-hon/",
"title": "Gary Hon, UT"
},
"measurement_sets": [
{
"@id": "/measurement-sets/IGVFDS8701ERXN/",
"accession": "IGVFDS8701ERXN",
"aliases": [
"gary-hon:CM_Pilot_2_PB_RNA_LW238"
],
"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/IGVFSM9326DRHX/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM9326DRHX",
"aliases": [
"nikhil-munshi:differentited_WTC11_CM_Pilot1_PB_LW238"
],
"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, transfected 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": "2024-02-21T18:35:52.524926+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": "1c5c9ca1-99b7-4615-88fe-a2da7f294f17"
}