{
"@context": "/terms/",
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"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS8280AMDA",
"aliases": [
"gary-hon:TF_Perturb_Seq_Pilot_Lenti_CM_sgRNA_LW277"
],
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS8280AMDA](/auxiliary-sets/IGVFDS8280AMDA/) has sequence file(s) [IGVFFI6637VQNC](/sequence-files/IGVFFI6637VQNC/), [IGVFFI9225ZAYG](/sequence-files/IGVFFI9225ZAYG/), [IGVFFI7205PTPJ](/sequence-files/IGVFFI7205PTPJ/), [IGVFFI0105QRUB](/sequence-files/IGVFFI0105QRUB/), [IGVFFI5482SCRU](/sequence-files/IGVFFI5482SCRU/), [IGVFFI4436NITM](/sequence-files/IGVFFI4436NITM/), [IGVFFI5870FWJX](/sequence-files/IGVFFI5870FWJX/), [IGVFFI4422CQQU](/sequence-files/IGVFFI4422CQQU/) 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/IGVFDS8280AMDA/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS8280AMDA](/auxiliary-sets/IGVFDS8280AMDA/) has sequence file(s): [IGVFFI6637VQNC](/sequence-files/IGVFFI6637VQNC/), [IGVFFI9225ZAYG](/sequence-files/IGVFFI9225ZAYG/), [IGVFFI7205PTPJ](/sequence-files/IGVFFI7205PTPJ/), [IGVFFI0105QRUB](/sequence-files/IGVFFI0105QRUB/), [IGVFFI5482SCRU](/sequence-files/IGVFFI5482SCRU/), [IGVFFI4436NITM](/sequence-files/IGVFFI4436NITM/), [IGVFFI5870FWJX](/sequence-files/IGVFFI5870FWJX/), [IGVFFI4422CQQU](/sequence-files/IGVFFI4422CQQU/) 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/IGVFDS8280AMDA/"
}
]
},
"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": "2024-02-21T21:01:45.684040+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": "IGVFFI6637VQNC",
"aliases": [
"gary-hon:LW277B-3_1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-01T17:05:50.811810+00:00",
"file_format": "fastq",
"file_size": 199086199,
"href": "/sequence-files/IGVFFI6637VQNC/@@download/IGVFFI6637VQNC.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/01/6dd4687e-e695-4159-8eca-2517425b7789/IGVFFI6637VQNC.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0010963/",
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-10-05-McDermott-NextSeq.10X/2023-10-05/outs/fastq_path/AAC7VLGHV/LW277B-3_S23_L001_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9225ZAYG/",
"accession": "IGVFFI9225ZAYG",
"aliases": [
"gary-hon:LW277B-3_1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-01T17:05:57.255655+00:00",
"file_format": "fastq",
"file_size": 219894034,
"href": "/sequence-files/IGVFFI9225ZAYG/@@download/IGVFFI9225ZAYG.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/01/d12ef297-ee41-4193-827e-d60242b2217e/IGVFFI9225ZAYG.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0010963/",
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-10-05-McDermott-NextSeq.10X/2023-10-05/outs/fastq_path/AAC7VLGHV/LW277B-3_S23_L001_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7205PTPJ/",
"accession": "IGVFFI7205PTPJ",
"aliases": [
"gary-hon:LW277B-3_1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-01T17:06:02.952921+00:00",
"file_format": "fastq",
"file_size": 657760890,
"href": "/sequence-files/IGVFFI7205PTPJ/@@download/IGVFFI7205PTPJ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/01/9f071aa2-e893-4a4e-a9c0-4890a3cdd02b/IGVFFI7205PTPJ.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0010963/",
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-10-05-McDermott-NextSeq.10X/2023-10-05/outs/fastq_path/AAC7VLGHV/LW277B-3_S23_L001_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0105QRUB/",
"accession": "IGVFFI0105QRUB",
"aliases": [
"gary-hon:LW277B-3_1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-01T17:06:12.500222+00:00",
"file_format": "fastq",
"file_size": 716846691,
"href": "/sequence-files/IGVFFI0105QRUB/@@download/IGVFFI0105QRUB.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/01/4023cc90-fabd-49f9-bcf4-88bd5e414221/IGVFFI0105QRUB.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0010963/",
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-10-05-McDermott-NextSeq.10X/2023-10-05/outs/fastq_path/AAC7VLGHV/LW277B-3_S23_L001_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5482SCRU/",
"accession": "IGVFFI5482SCRU",
"aliases": [
"gary-hon:LW277B-3_2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-01T17:06:22.530662+00:00",
"file_format": "fastq",
"file_size": 183560459,
"href": "/sequence-files/IGVFFI5482SCRU/@@download/IGVFFI5482SCRU.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/01/eff650ac-b7b2-4158-b9d6-2e9a1f492ec1/IGVFFI5482SCRU.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0010963/",
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-10-05-McDermott-NextSeq.10X/2023-10-05/outs/fastq_path/AAC7VLGHV/LW277B-3_S23_L002_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4436NITM/",
"accession": "IGVFFI4436NITM",
"aliases": [
"gary-hon:LW277B-3_2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-01T17:06:27.984380+00:00",
"file_format": "fastq",
"file_size": 207878626,
"href": "/sequence-files/IGVFFI4436NITM/@@download/IGVFFI4436NITM.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/01/5b3f53e9-e808-4843-9bf7-c121db24efcf/IGVFFI4436NITM.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0010963/",
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-10-05-McDermott-NextSeq.10X/2023-10-05/outs/fastq_path/AAC7VLGHV/LW277B-3_S23_L002_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5870FWJX/",
"accession": "IGVFFI5870FWJX",
"aliases": [
"gary-hon:LW277B-3_2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-01T17:06:33.677194+00:00",
"file_format": "fastq",
"file_size": 629608398,
"href": "/sequence-files/IGVFFI5870FWJX/@@download/IGVFFI5870FWJX.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/01/442a0b04-fa52-4ab9-889c-37d0a558b328/IGVFFI5870FWJX.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0010963/",
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-10-05-McDermott-NextSeq.10X/2023-10-05/outs/fastq_path/AAC7VLGHV/LW277B-3_S23_L002_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4422CQQU/",
"accession": "IGVFFI4422CQQU",
"aliases": [
"gary-hon:LW277B-3_2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-01T17:06:42.998523+00:00",
"file_format": "fastq",
"file_size": 677426753,
"href": "/sequence-files/IGVFFI4422CQQU/@@download/IGVFFI4422CQQU.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/01/fc9f241e-7e3f-419c-a97c-3c2772a8f28f/IGVFFI4422CQQU.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0010963/",
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-10-05-McDermott-NextSeq.10X/2023-10-05/outs/fastq_path/AAC7VLGHV/LW277B-3_S23_L002_R2_001.fastq.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS4389OUWU/"
],
"lab": {
"@id": "/labs/gary-hon/",
"title": "Gary Hon, UT"
},
"measurement_sets": [
{
"@id": "/measurement-sets/IGVFDS7834BXBN/",
"accession": "IGVFDS7834BXBN",
"aliases": [
"gary-hon:TF_Perturb_Seq_Pilot_Lenti_CM_LW277"
],
"preferred_assay_title": "Perturb-seq",
"status": "preview"
}
],
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM7513BJDT/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM7513BJDT",
"aliases": [
"nikhil-munshi:differentited_WTC11_TF_Perturb_Seq_Pilot_CMs_Lenti_LW277"
],
"classifications": [
"differentiated cell specimen"
],
"construct_library_sets": [
"/construct-library-sets/IGVFDS2302LCEO/"
],
"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_LW277), 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": "2024-03-01T17:05:50.811810+00:00",
"summary": "gRNA sequencing for CRISPR interference Perturb-seq integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"uuid": "53433a0d-00d1-458c-b926-17f157cd4f33"
}