{
"@context": "/terms/",
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"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS7019VPKV",
"aliases": [
"gary-hon:CM_Pilot_2_PB_sgRNA_LW238"
],
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS7019VPKV](/auxiliary-sets/IGVFDS7019VPKV/) has sequence file(s) [IGVFFI5790IQTB](/sequence-files/IGVFFI5790IQTB/), [IGVFFI0279NKCJ](/sequence-files/IGVFFI0279NKCJ/), [IGVFFI8978ELVT](/sequence-files/IGVFFI8978ELVT/), [IGVFFI7459ZLGX](/sequence-files/IGVFFI7459ZLGX/), [IGVFFI3499NNMI](/sequence-files/IGVFFI3499NNMI/), [IGVFFI1992QYNR](/sequence-files/IGVFFI1992QYNR/), [IGVFFI6560RTAA](/sequence-files/IGVFFI6560RTAA/), [IGVFFI8362NKUV](/sequence-files/IGVFFI8362NKUV/) 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/IGVFDS7019VPKV/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS7019VPKV](/auxiliary-sets/IGVFDS7019VPKV/) has sequence file(s): [IGVFFI5790IQTB](/sequence-files/IGVFFI5790IQTB/), [IGVFFI0279NKCJ](/sequence-files/IGVFFI0279NKCJ/), [IGVFFI8978ELVT](/sequence-files/IGVFFI8978ELVT/), [IGVFFI7459ZLGX](/sequence-files/IGVFFI7459ZLGX/), [IGVFFI3499NNMI](/sequence-files/IGVFFI3499NNMI/), [IGVFFI1992QYNR](/sequence-files/IGVFFI1992QYNR/), [IGVFFI6560RTAA](/sequence-files/IGVFFI6560RTAA/), [IGVFFI8362NKUV](/sequence-files/IGVFFI8362NKUV/) 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/IGVFDS7019VPKV/"
}
]
},
"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": "2024-02-15T23:35:48.284597+00:00",
"donors": [
{
"@id": "/human-donors/IGVFDO1756PPKO/",
"accession": "IGVFDO1756PPKO",
"aliases": [
"igvf:donor_of_WTC11"
],
"sex": "male",
"status": "released",
"taxa": "Homo sapiens"
}
],
"file_set_type": "gRNA sequencing",
"files": [
{
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"accession": "IGVFFI5790IQTB",
"aliases": [
"gary-hon:LW238B-2_1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-21T18:34:48.598576+00:00",
"file_format": "fastq",
"file_size": 1609977070,
"href": "/sequence-files/IGVFFI5790IQTB/@@download/IGVFFI5790IQTB.fastq.gz",
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"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/LW238B-2_S8_L001_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0279NKCJ/",
"accession": "IGVFFI0279NKCJ",
"aliases": [
"gary-hon:LW238B-2_2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-21T18:35:21.860408+00:00",
"file_format": "fastq",
"file_size": 1146520509,
"href": "/sequence-files/IGVFFI0279NKCJ/@@download/IGVFFI0279NKCJ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/21/da1b9ece-650f-4f7f-ad4b-bd1c1f01ebc2/IGVFFI0279NKCJ.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/LW238B-2_S8_L002_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8978ELVT/",
"accession": "IGVFFI8978ELVT",
"aliases": [
"gary-hon:LW238B-2_2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-21T18:35:35.881756+00:00",
"file_format": "fastq",
"file_size": 1477502231,
"href": "/sequence-files/IGVFFI8978ELVT/@@download/IGVFFI8978ELVT.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/21/80b7676c-56fc-4aed-b343-cd4f6a8153c9/IGVFFI8978ELVT.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/LW238B-2_S8_L002_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7459ZLGX/",
"accession": "IGVFFI7459ZLGX",
"aliases": [
"gary-hon:LW238B-2_1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-21T18:34:11.442738+00:00",
"file_format": "fastq",
"file_size": 360165925,
"href": "/sequence-files/IGVFFI7459ZLGX/@@download/IGVFFI7459ZLGX.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/21/0d82b6f7-3f52-42d8-a1d1-cfdac7063076/IGVFFI7459ZLGX.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/LW238B-2_S8_L001_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3499NNMI/",
"accession": "IGVFFI3499NNMI",
"aliases": [
"gary-hon:LW238B-2_1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-21T18:34:19.231488+00:00",
"file_format": "fastq",
"file_size": 363962874,
"href": "/sequence-files/IGVFFI3499NNMI/@@download/IGVFFI3499NNMI.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/21/4608e3a1-74d3-45df-a89f-cc4d1f068d25/IGVFFI3499NNMI.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/LW238B-2_S8_L001_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1992QYNR/",
"accession": "IGVFFI1992QYNR",
"aliases": [
"gary-hon:LW238B-2_1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-21T18:34:31.162906+00:00",
"file_format": "fastq",
"file_size": 1243619790,
"href": "/sequence-files/IGVFFI1992QYNR/@@download/IGVFFI1992QYNR.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/21/c0114a67-53d2-4b1e-b4a9-2ea46602d251/IGVFFI1992QYNR.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/LW238B-2_S8_L001_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6560RTAA/",
"accession": "IGVFFI6560RTAA",
"aliases": [
"gary-hon:LW238B-2_2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-21T18:35:14.373444+00:00",
"file_format": "fastq",
"file_size": 328025057,
"href": "/sequence-files/IGVFFI6560RTAA/@@download/IGVFFI6560RTAA.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/21/a3a51e3f-f1f5-4f8f-a321-21e4b048ffcb/IGVFFI6560RTAA.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/LW238B-2_S8_L002_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8362NKUV/",
"accession": "IGVFFI8362NKUV",
"aliases": [
"gary-hon:LW238B-2_2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-21T18:35:07.354176+00:00",
"file_format": "fastq",
"file_size": 325448056,
"href": "/sequence-files/IGVFFI8362NKUV/@@download/IGVFFI8362NKUV.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/21/384d3399-812a-4154-8a24-ba7a63ea80c7/IGVFFI8362NKUV.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/LW238B-2_S8_L002_I1_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"
}
],
"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": "2024-02-21T18:34:11.442738+00:00",
"summary": "gRNA sequencing for CRISPR interference Perturb-seq integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"uuid": "eb1b8d87-7b4b-4164-be81-92e7e8f96e15"
}