{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS3945FAEL/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS3945FAEL",
"aliases": [
"charles-gersbach:cd8-tcells-perturb-seq-crispra-grna-rep3"
],
"audit": {
"WARNING": [
{
"category": "missing age",
"detail": "Primary cell [IGVFSM2105CLXS](/primary-cells/IGVFSM2105CLXS/) is missing `upper_bound_age`, `lower_bound_age`, and `age_units`. Tissues, primary cells, and whole organisms are expected to specify a lower bound age, upper bound age, and age units.",
"level": 40,
"level_name": "WARNING",
"name": "audit_biosample_age",
"path": "/primary-cells/IGVFSM2105CLXS/"
}
]
},
"award": {
"@id": "/awards/HG012053/",
"component": "functional characterization",
"contact_pi": {
"@id": "/users/5d329c0e-3ea9-49bf-9bb9-844a53a882c0/",
"title": "Charles Gersbach"
},
"title": "High-Throughput Functional Annotation of Gene Regulatory Elements and Variants Critical to Complex Cellular Phenotypes"
},
"control_for": [],
"creation_timestamp": "2023-11-08T19:41:48.538766+00:00",
"donors": [
{
"@id": "/human-donors/IGVFDO4425KRAT/",
"accession": "IGVFDO4425KRAT",
"aliases": [
"charles-gersbach:cd8-tcells-donor-8"
],
"sex": "unspecified",
"status": "released",
"taxa": "Homo sapiens"
}
],
"file_set_type": "gRNA sequencing",
"files": [
{
"@id": "/sequence-files/IGVFFI1328IASZ/",
"accession": "IGVFFI1328IASZ",
"aliases": [
"charles-gersbach:cd8-tcells-perturb-seq-crispra-grna-rep3-rep3-fastq-lane1-R1"
],
"content_type": "reads",
"creation_timestamp": "2023-11-09T19:31:29.209889+00:00",
"file_format": "fastq",
"file_size": 1337473537,
"href": "/sequence-files/IGVFFI1328IASZ/@@download/IGVFFI1328IASZ.fastq.gz",
"s3_uri": "s3://igvf-files/2023/11/09/e0c0aa74-ff8b-4fa5-83bf-fc97f76bce6a/IGVFFI1328IASZ.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008637/",
"submitted_file_name": "/data/reddylab/Alex/IGVF/data_submissions/raw_data/AIM_2_T_cell_project_1/gRNA_CRISPRa_D3_S12_L001_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7135VSEK/",
"accession": "IGVFFI7135VSEK",
"aliases": [
"charles-gersbach:cd8-tcells-perturb-seq-crispra-grna-rep3-rep3-fastq-lane2-R2"
],
"content_type": "reads",
"creation_timestamp": "2023-11-09T19:41:25.458895+00:00",
"file_format": "fastq",
"file_size": 2475398740,
"href": "/sequence-files/IGVFFI7135VSEK/@@download/IGVFFI7135VSEK.fastq.gz",
"s3_uri": "s3://igvf-files/2023/11/09/4b345969-4d63-4b6f-a677-347a89b251b6/IGVFFI7135VSEK.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008637/",
"submitted_file_name": "/data/reddylab/Alex/IGVF/data_submissions/raw_data/AIM_2_T_cell_project_1/gRNA_CRISPRa_D3_S12_L002_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3786SYLP/",
"accession": "IGVFFI3786SYLP",
"aliases": [
"charles-gersbach:cd8-tcells-perturb-seq-crispra-grna-rep3-rep3-fastq-lane2-R1"
],
"content_type": "reads",
"creation_timestamp": "2023-11-09T19:31:45.348392+00:00",
"file_format": "fastq",
"file_size": 1318828540,
"href": "/sequence-files/IGVFFI3786SYLP/@@download/IGVFFI3786SYLP.fastq.gz",
"s3_uri": "s3://igvf-files/2023/11/09/cecc3c19-6e75-4da1-9425-d92c470dba8b/IGVFFI3786SYLP.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008637/",
"submitted_file_name": "/data/reddylab/Alex/IGVF/data_submissions/raw_data/AIM_2_T_cell_project_1/gRNA_CRISPRa_D3_S12_L002_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3652DBNT/",
"accession": "IGVFFI3652DBNT",
"aliases": [
"charles-gersbach:cd8-tcells-perturb-seq-crispra-grna-rep3-rep3-fastq-lane3-R2"
],
"content_type": "reads",
"creation_timestamp": "2023-11-09T19:41:51.283265+00:00",
"file_format": "fastq",
"file_size": 2492268603,
"href": "/sequence-files/IGVFFI3652DBNT/@@download/IGVFFI3652DBNT.fastq.gz",
"s3_uri": "s3://igvf-files/2023/11/09/92f93e1d-90e7-403a-9b49-730fab6237b1/IGVFFI3652DBNT.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008637/",
"submitted_file_name": "/data/reddylab/Alex/IGVF/data_submissions/raw_data/AIM_2_T_cell_project_1/gRNA_CRISPRa_D3_S12_L003_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2032UXJP/",
"accession": "IGVFFI2032UXJP",
"aliases": [
"charles-gersbach:cd8-tcells-perturb-seq-crispra-grna-rep3-rep3-fastq-lane1-R2"
],
"content_type": "reads",
"creation_timestamp": "2023-11-09T19:40:59.027129+00:00",
"file_format": "fastq",
"file_size": 2521811101,
"href": "/sequence-files/IGVFFI2032UXJP/@@download/IGVFFI2032UXJP.fastq.gz",
"s3_uri": "s3://igvf-files/2023/11/09/d9f72cbc-4eb6-4f68-9377-6924356f5af1/IGVFFI2032UXJP.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008637/",
"submitted_file_name": "/data/reddylab/Alex/IGVF/data_submissions/raw_data/AIM_2_T_cell_project_1/gRNA_CRISPRa_D3_S12_L001_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8543ICNA/",
"accession": "IGVFFI8543ICNA",
"aliases": [
"charles-gersbach:cd8-tcells-perturb-seq-crispra-grna-rep3-rep3-fastq-lane4-R2"
],
"content_type": "reads",
"creation_timestamp": "2023-11-09T19:42:16.997599+00:00",
"file_format": "fastq",
"file_size": 2484576334,
"href": "/sequence-files/IGVFFI8543ICNA/@@download/IGVFFI8543ICNA.fastq.gz",
"s3_uri": "s3://igvf-files/2023/11/09/08b5fec0-a7bb-47cb-b6ea-0e077444d918/IGVFFI8543ICNA.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008637/",
"submitted_file_name": "/data/reddylab/Alex/IGVF/data_submissions/raw_data/AIM_2_T_cell_project_1/gRNA_CRISPRa_D3_S12_L004_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2506CIAV/",
"accession": "IGVFFI2506CIAV",
"aliases": [
"charles-gersbach:cd8-tcells-perturb-seq-crispra-grna-rep3-rep3-fastq-lane3-R1"
],
"content_type": "reads",
"creation_timestamp": "2023-11-09T19:32:01.674767+00:00",
"file_format": "fastq",
"file_size": 1327620854,
"href": "/sequence-files/IGVFFI2506CIAV/@@download/IGVFFI2506CIAV.fastq.gz",
"s3_uri": "s3://igvf-files/2023/11/09/2b2a59d0-7709-4c2c-adda-dcc4680efb05/IGVFFI2506CIAV.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008637/",
"submitted_file_name": "/data/reddylab/Alex/IGVF/data_submissions/raw_data/AIM_2_T_cell_project_1/gRNA_CRISPRa_D3_S12_L003_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2756XAJA/",
"accession": "IGVFFI2756XAJA",
"aliases": [
"charles-gersbach:cd8-tcells-perturb-seq-crispra-grna-rep3-rep3-fastq-lane4-R1"
],
"content_type": "reads",
"creation_timestamp": "2023-11-09T19:32:17.847496+00:00",
"file_format": "fastq",
"file_size": 1322826070,
"href": "/sequence-files/IGVFFI2756XAJA/@@download/IGVFFI2756XAJA.fastq.gz",
"s3_uri": "s3://igvf-files/2023/11/09/3d838ea2-0d07-4ab2-9d47-cac0a6604820/IGVFFI2756XAJA.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008637/",
"submitted_file_name": "/data/reddylab/Alex/IGVF/data_submissions/raw_data/AIM_2_T_cell_project_1/gRNA_CRISPRa_D3_S12_L004_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI0628YCXP/",
"accession": "IGVFFI0628YCXP",
"aliases": [
"charles-gersbach:cd8-tcells-perturb-seq-crispra-grna-rep3-rep3-fastq-lane2_seqspec"
],
"content_type": "seqspec",
"creation_timestamp": "2024-09-20T16:50:02.101519+00:00",
"file_format": "yaml",
"file_size": 1079,
"href": "/configuration-files/IGVFFI0628YCXP/@@download/IGVFFI0628YCXP.yaml.gz",
"s3_uri": "s3://igvf-files/2024/09/20/f32af5be-1931-4bd8-ae36-bf9c94ff3c40/IGVFFI0628YCXP.yaml.gz",
"submitted_file_name": "/datacommons/gersbachlab/Ruhi/IGVFseqspec/CRISPRaD3_S6nS12_L002.crispr.yaml.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI0583TWJA/",
"accession": "IGVFFI0583TWJA",
"aliases": [
"charles-gersbach:cd8-tcells-perturb-seq-crispra-grna-rep3-rep3-fastq-lane1_seqspec"
],
"content_type": "seqspec",
"creation_timestamp": "2024-09-20T16:49:59.700354+00:00",
"file_format": "yaml",
"file_size": 1078,
"href": "/configuration-files/IGVFFI0583TWJA/@@download/IGVFFI0583TWJA.yaml.gz",
"s3_uri": "s3://igvf-files/2024/09/20/0d113415-936c-4759-b9f0-a22567c60c9c/IGVFFI0583TWJA.yaml.gz",
"submitted_file_name": "/datacommons/gersbachlab/Ruhi/IGVFseqspec/CRISPRaD3_S6nS12_L001.crispr.yaml.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI2494UMAV/",
"accession": "IGVFFI2494UMAV",
"aliases": [
"charles-gersbach:cd8-tcells-perturb-seq-crispra-grna-rep3-rep3-fastq-lane3_seqspec"
],
"content_type": "seqspec",
"creation_timestamp": "2024-09-20T16:50:03.920887+00:00",
"file_format": "yaml",
"file_size": 1079,
"href": "/configuration-files/IGVFFI2494UMAV/@@download/IGVFFI2494UMAV.yaml.gz",
"s3_uri": "s3://igvf-files/2024/09/20/7deb74a4-4e0f-42fe-b340-e4f80be07662/IGVFFI2494UMAV.yaml.gz",
"submitted_file_name": "/datacommons/gersbachlab/Ruhi/IGVFseqspec/CRISPRaD3_S6nS12_L003.crispr.yaml.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI2907BHMS/",
"accession": "IGVFFI2907BHMS",
"aliases": [
"charles-gersbach:cd8-tcells-perturb-seq-crispra-grna-rep3-rep3-fastq-lane4_seqspec"
],
"content_type": "seqspec",
"creation_timestamp": "2024-09-20T16:50:05.826855+00:00",
"file_format": "yaml",
"file_size": 1079,
"href": "/configuration-files/IGVFFI2907BHMS/@@download/IGVFFI2907BHMS.yaml.gz",
"s3_uri": "s3://igvf-files/2024/09/20/587f84e4-d1df-4973-80a3-6a78439bca27/IGVFFI2907BHMS.yaml.gz",
"submitted_file_name": "/datacommons/gersbachlab/Ruhi/IGVFseqspec/CRISPRaD3_S6nS12_L004.crispr.yaml.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS4011VZXE/"
],
"lab": {
"@id": "/labs/charles-gersbach/",
"title": "Charles Gersbach, Duke"
},
"measurement_sets": [
{
"@id": "/measurement-sets/IGVFDS0238VKNF/",
"accession": "IGVFDS0238VKNF",
"aliases": [
"charles-gersbach:cd8-tcells-perturb-seq-crispra-gex-rep3"
],
"preferred_assay_title": "Perturb-seq"
}
],
"publications": [
{
"@id": "/publications/6cc80a53-4ca1-4bd4-9942-f0f335b7ec20/",
"publication_identifiers": [
"PMID:37945901",
"doi:10.1038/s41588-023-01554-0",
"PMCID:PMC10703699"
]
}
],
"release_timestamp": "2024-10-18T19:49:56.522323+00:00",
"samples": [
{
"@id": "/primary-cells/IGVFSM2105CLXS/",
"@type": [
"PrimaryCell",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM2105CLXS",
"aliases": [
"charles-gersbach:cd8-tcells-primary-cell-crispra-rep3"
],
"classifications": [
"primary cell"
],
"construct_library_sets": [
"/construct-library-sets/IGVFDS0821YMMV/"
],
"modifications": [
{
"@id": "/crispr-modifications/2c49eb31-f10b-47b7-b260-4f720014ad79/",
"modality": "activation"
}
],
"sample_terms": [
{
"@id": "/sample-terms/CL_0000909/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"status": "released",
"summary": "CD8-positive, alpha-beta memory T cell",
"term_name": "CD8-positive, alpha-beta memory T cell"
}
],
"status": "released",
"summary": "CD8-positive, alpha-beta memory T cell, Homo sapiens modified with CRISPRa Sa-dCas9-VP64, transduced (lentivirus) with a guide library (MOI of 0.4)",
"taxa": "Homo sapiens"
}
],
"schema_version": "11",
"status": "released",
"submitted_by": {
"@id": "/users/29f5f78d-ac90-421e-90c6-a90e1dc407a7/",
"title": "Alejandro Barrera"
},
"submitted_files_timestamp": "2023-11-09T19:31:29.209889+00:00",
"summary": "gRNA sequencing for activation Perturb-seq integrating a guide (sgRNA) library targeting transcription start sites in 24 genes",
"uuid": "ba0c5207-57ea-4064-b6d8-0a16d91d3351"
}