{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS1726RJYG/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS1726RJYG",
"aliases": [
"gary-hon:CM_Pilot_2_PB_HTO_LW235"
],
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS1726RJYG](/auxiliary-sets/IGVFDS1726RJYG/) has sequence file(s) [IGVFFI7079PLNF](/sequence-files/IGVFFI7079PLNF/), [IGVFFI2341UENO](/sequence-files/IGVFFI2341UENO/), [IGVFFI8384IQXK](/sequence-files/IGVFFI8384IQXK/), [IGVFFI1205FYWX](/sequence-files/IGVFFI1205FYWX/), [IGVFFI3013ZQOT](/sequence-files/IGVFFI3013ZQOT/), [IGVFFI8956XELZ](/sequence-files/IGVFFI8956XELZ/), [IGVFFI5494FVJF](/sequence-files/IGVFFI5494FVJF/), [IGVFFI3707CIKC](/sequence-files/IGVFFI3707CIKC/) 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/IGVFDS1726RJYG/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS1726RJYG](/auxiliary-sets/IGVFDS1726RJYG/) has sequence file(s): [IGVFFI7079PLNF](/sequence-files/IGVFFI7079PLNF/), [IGVFFI2341UENO](/sequence-files/IGVFFI2341UENO/), [IGVFFI8384IQXK](/sequence-files/IGVFFI8384IQXK/), [IGVFFI1205FYWX](/sequence-files/IGVFFI1205FYWX/), [IGVFFI3013ZQOT](/sequence-files/IGVFFI3013ZQOT/), [IGVFFI8956XELZ](/sequence-files/IGVFFI8956XELZ/), [IGVFFI5494FVJF](/sequence-files/IGVFFI5494FVJF/), [IGVFFI3707CIKC](/sequence-files/IGVFFI3707CIKC/) 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/IGVFDS1726RJYG/"
}
]
},
"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": "2024-02-15T23:35:40.060034+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/IGVFFI7079PLNF/",
"accession": "IGVFFI7079PLNF",
"aliases": [
"gary-hon:LW235C_2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-21T18:29:24.531329+00:00",
"file_format": "fastq",
"file_size": 646574327,
"href": "/sequence-files/IGVFFI7079PLNF/@@download/IGVFFI7079PLNF.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/21/2d32d99b-cf26-4bfb-93c4-d9948cc59c28/IGVFFI7079PLNF.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/LW235C_S13_L002_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2341UENO/",
"accession": "IGVFFI2341UENO",
"aliases": [
"gary-hon:LW235C_1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-21T18:28:39.398828+00:00",
"file_format": "fastq",
"file_size": 111502116,
"href": "/sequence-files/IGVFFI2341UENO/@@download/IGVFFI2341UENO.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/21/dcaccd10-483d-4c44-9585-2b9719b8d6bb/IGVFFI2341UENO.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/LW235C_S13_L001_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8384IQXK/",
"accession": "IGVFFI8384IQXK",
"aliases": [
"gary-hon:LW235C_2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-21T18:29:12.593762+00:00",
"file_format": "fastq",
"file_size": 101321725,
"href": "/sequence-files/IGVFFI8384IQXK/@@download/IGVFFI8384IQXK.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/21/20625838-c6dd-4cb5-b93e-24380d73f501/IGVFFI8384IQXK.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/LW235C_S13_L002_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1205FYWX/",
"accession": "IGVFFI1205FYWX",
"aliases": [
"gary-hon:LW235C_1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-21T18:28:34.101599+00:00",
"file_format": "fastq",
"file_size": 123760993,
"href": "/sequence-files/IGVFFI1205FYWX/@@download/IGVFFI1205FYWX.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/21/7f20a4ad-3d95-4c2f-97f9-3e0bd6414727/IGVFFI1205FYWX.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/LW235C_S13_L001_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3013ZQOT/",
"accession": "IGVFFI3013ZQOT",
"aliases": [
"gary-hon:LW235C_1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-21T18:28:52.632040+00:00",
"file_format": "fastq",
"file_size": 702432504,
"href": "/sequence-files/IGVFFI3013ZQOT/@@download/IGVFFI3013ZQOT.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/21/54d458e0-fbb9-452d-b0f0-20828699d690/IGVFFI3013ZQOT.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/LW235C_S13_L001_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8956XELZ/",
"accession": "IGVFFI8956XELZ",
"aliases": [
"gary-hon:LW235C_2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-21T18:29:17.484249+00:00",
"file_format": "fastq",
"file_size": 351595986,
"href": "/sequence-files/IGVFFI8956XELZ/@@download/IGVFFI8956XELZ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/21/c7be496c-2f44-4d7c-b68d-065377b5a1a0/IGVFFI8956XELZ.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/LW235C_S13_L002_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5494FVJF/",
"accession": "IGVFFI5494FVJF",
"aliases": [
"gary-hon:LW235C_2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-21T18:29:07.257117+00:00",
"file_format": "fastq",
"file_size": 114010083,
"href": "/sequence-files/IGVFFI5494FVJF/@@download/IGVFFI5494FVJF.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/21/5db6c4e4-4bc6-4ecb-9eab-5633cc880ba8/IGVFFI5494FVJF.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/LW235C_S13_L002_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3707CIKC/",
"accession": "IGVFFI3707CIKC",
"aliases": [
"gary-hon:LW235C_1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-21T18:28:44.553717+00:00",
"file_format": "fastq",
"file_size": 380015063,
"href": "/sequence-files/IGVFFI3707CIKC/@@download/IGVFFI3707CIKC.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/21/690beb64-e74c-4f7a-9deb-46cc1facdf4b/IGVFFI3707CIKC.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/LW235C_S13_L001_R1_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/IGVFDS1663ZHVE/",
"accession": "IGVFDS1663ZHVE",
"aliases": [
"gary-hon:CM_Pilot_2_PB_RNA_LW235"
],
"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/IGVFSM2930BIPX/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM2930BIPX",
"aliases": [
"nikhil-munshi:differentited_WTC11_CM_Pilot1_PB_LW235"
],
"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_LW265), 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": "2024-02-21T18:28:34.101599+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": "ca159fdf-ba9f-4434-b8c4-3d8897c8ee3c"
}