{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS9925GTMC/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS9925GTMC",
"aliases": [
"gary-hon:CM_Pilot_2_PB_HTO_LW236"
],
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS9925GTMC](/auxiliary-sets/IGVFDS9925GTMC/) has sequence file(s) [IGVFFI7364IONS](/sequence-files/IGVFFI7364IONS/), [IGVFFI7549VRUY](/sequence-files/IGVFFI7549VRUY/), [IGVFFI9116NYPQ](/sequence-files/IGVFFI9116NYPQ/), [IGVFFI5839AQOX](/sequence-files/IGVFFI5839AQOX/), [IGVFFI5160RFGF](/sequence-files/IGVFFI5160RFGF/), [IGVFFI7687IOMO](/sequence-files/IGVFFI7687IOMO/), [IGVFFI5328JRCC](/sequence-files/IGVFFI5328JRCC/), [IGVFFI3400AXGE](/sequence-files/IGVFFI3400AXGE/) 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/IGVFDS9925GTMC/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS9925GTMC](/auxiliary-sets/IGVFDS9925GTMC/) has sequence file(s): [IGVFFI7364IONS](/sequence-files/IGVFFI7364IONS/), [IGVFFI7549VRUY](/sequence-files/IGVFFI7549VRUY/), [IGVFFI9116NYPQ](/sequence-files/IGVFFI9116NYPQ/), [IGVFFI5839AQOX](/sequence-files/IGVFFI5839AQOX/), [IGVFFI5160RFGF](/sequence-files/IGVFFI5160RFGF/), [IGVFFI7687IOMO](/sequence-files/IGVFFI7687IOMO/), [IGVFFI5328JRCC](/sequence-files/IGVFFI5328JRCC/), [IGVFFI3400AXGE](/sequence-files/IGVFFI3400AXGE/) 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/IGVFDS9925GTMC/"
}
]
},
"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": "2024-02-15T23:35:42.084009+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/IGVFFI7364IONS/",
"accession": "IGVFFI7364IONS",
"aliases": [
"gary-hon:LW236C_2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-21T18:31:08.057435+00:00",
"file_format": "fastq",
"file_size": 132063800,
"href": "/sequence-files/IGVFFI7364IONS/@@download/IGVFFI7364IONS.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/21/d26af885-2fd2-4ed8-943e-9c43238c6a8d/IGVFFI7364IONS.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/LW236C_S14_L002_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7549VRUY/",
"accession": "IGVFFI7549VRUY",
"aliases": [
"gary-hon:LW236C_2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-21T18:31:13.827179+00:00",
"file_format": "fastq",
"file_size": 400781001,
"href": "/sequence-files/IGVFFI7549VRUY/@@download/IGVFFI7549VRUY.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/21/e8fc14c6-7875-454c-b8de-5b6045861f9f/IGVFFI7549VRUY.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/LW236C_S14_L002_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9116NYPQ/",
"accession": "IGVFFI9116NYPQ",
"aliases": [
"gary-hon:LW236C_1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-21T18:30:51.107763+00:00",
"file_format": "fastq",
"file_size": 807109425,
"href": "/sequence-files/IGVFFI9116NYPQ/@@download/IGVFFI9116NYPQ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/21/be113d3a-8ad9-4182-85a1-7bb788cba425/IGVFFI9116NYPQ.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/LW236C_S14_L001_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5839AQOX/",
"accession": "IGVFFI5839AQOX",
"aliases": [
"gary-hon:LW236C_1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-21T18:30:37.283973+00:00",
"file_format": "fastq",
"file_size": 143267975,
"href": "/sequence-files/IGVFFI5839AQOX/@@download/IGVFFI5839AQOX.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/21/42535871-2e5b-4722-8346-c68ed8e8dd27/IGVFFI5839AQOX.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/LW236C_S14_L001_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5160RFGF/",
"accession": "IGVFFI5160RFGF",
"aliases": [
"gary-hon:LW236C_1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-21T18:30:42.979539+00:00",
"file_format": "fastq",
"file_size": 437883233,
"href": "/sequence-files/IGVFFI5160RFGF/@@download/IGVFFI5160RFGF.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/21/38793b06-9d66-4905-ae50-d3727dbc714d/IGVFFI5160RFGF.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/LW236C_S14_L001_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7687IOMO/",
"accession": "IGVFFI7687IOMO",
"aliases": [
"gary-hon:LW236C_2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-21T18:31:02.401364+00:00",
"file_format": "fastq",
"file_size": 137455412,
"href": "/sequence-files/IGVFFI7687IOMO/@@download/IGVFFI7687IOMO.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/21/7e25022c-2ae4-48f3-adf5-d7d492cdb71b/IGVFFI7687IOMO.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/LW236C_S14_L002_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5328JRCC/",
"accession": "IGVFFI5328JRCC",
"aliases": [
"gary-hon:LW236C_1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-21T18:30:31.773952+00:00",
"file_format": "fastq",
"file_size": 145092567,
"href": "/sequence-files/IGVFFI5328JRCC/@@download/IGVFFI5328JRCC.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/21/926325d2-fd1a-454e-ad79-0167d303ddac/IGVFFI5328JRCC.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/LW236C_S14_L001_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3400AXGE/",
"accession": "IGVFFI3400AXGE",
"aliases": [
"gary-hon:LW236C_2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-21T18:31:21.510562+00:00",
"file_format": "fastq",
"file_size": 736364147,
"href": "/sequence-files/IGVFFI3400AXGE/@@download/IGVFFI3400AXGE.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/21/a8205aa6-12fe-4da8-b092-600e29a6640e/IGVFFI3400AXGE.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/LW236C_S14_L002_R2_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/IGVFDS0890CUXC/",
"accession": "IGVFDS0890CUXC",
"aliases": [
"gary-hon:CM_Pilot_2_PB_RNA_LW236"
],
"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/IGVFSM5652SBGF/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM5652SBGF",
"aliases": [
"nikhil-munshi:differentited_WTC11_CM_Pilot1_PB_LW236"
],
"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, 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": "2024-02-21T18:30:31.773952+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": "d66fdb6f-130b-492a-b44c-766887ce8b57"
}