{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS9674AATW/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS9674AATW",
"aliases": [
"charles-gersbach:cd8-tcells-perturb-seq-crispri-gex-rep3"
],
"assay_term": {
"@id": "/assay-terms/OBI_0003660/",
"assay_slims": [
"CRISPR screens"
],
"status": "released",
"term_name": "in vitro CRISPR screen using single-cell RNA-seq"
},
"audit": {
"WARNING": [
{
"category": "missing age",
"detail": "Primary cell [IGVFSM5189UBOI](/primary-cells/IGVFSM5189UBOI/) 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/IGVFSM5189UBOI/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS0591VNKJ/",
"accession": "IGVFDS0591VNKJ",
"aliases": [
"charles-gersbach:cd8-tcells-perturb-seq-crispri-grna-rep3"
],
"file_set_type": "gRNA sequencing",
"status": "released"
}
],
"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"
},
"construct_library_sets": [
{
"@id": "/construct-library-sets/IGVFDS0821YMMV/",
"accession": "IGVFDS0821YMMV",
"file_set_type": "guide library",
"integrated_content_files": [
{
"@id": "/tabular-files/IGVFFI1405WMSH/",
"accession": "IGVFFI1405WMSH",
"content_type": "guide RNA sequences",
"status": "revoked",
"summary": "GRCh38 guide RNA sequences"
},
{
"@id": "/tabular-files/IGVFFI2489BLJI/",
"accession": "IGVFFI2489BLJI",
"content_type": "guide RNA sequences",
"status": "released",
"summary": "GRCh38 guide RNA sequences"
}
],
"status": "released",
"summary": "guide (sgRNA) library targeting transcription start sites in 24 genes"
}
],
"control_for": [],
"creation_timestamp": "2023-11-08T19:33:43.468360+00:00",
"donors": [
{
"@id": "/human-donors/IGVFDO4425KRAT/",
"accession": "IGVFDO4425KRAT",
"aliases": [
"charles-gersbach:cd8-tcells-donor-8"
],
"sex": "unspecified",
"status": "released",
"taxa": "Homo sapiens"
}
],
"externally_hosted": false,
"file_set_type": "experimental data",
"files": [
{
"@id": "/sequence-files/IGVFFI7880KEAK/",
"accession": "IGVFFI7880KEAK",
"aliases": [
"charles-gersbach:cd8-tcells-perturb-seq-crispri-gex-rep3-rep3-fastq-lane1-R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-11-09T01:07:05.239635+00:00",
"file_format": "fastq",
"file_size": 5706458241,
"href": "/sequence-files/IGVFFI7880KEAK/@@download/IGVFFI7880KEAK.fastq.gz",
"s3_uri": "s3://igvf-files/2023/11/09/ae7b6373-332c-48bf-8ef5-aac0875ce647/IGVFFI7880KEAK.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008637/",
"status": "released",
"term_name": "Illumina NovaSeq 6000"
},
"status": "released",
"submitted_file_name": "/data/reddylab/Alex/IGVF/data_submissions/raw_data/AIM_2_T_cell_project_1/GEX_CRISPRi_D3_S3_L001_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2055FUEP/",
"accession": "IGVFFI2055FUEP",
"aliases": [
"charles-gersbach:cd8-tcells-perturb-seq-crispri-gex-rep3-rep3-fastq-lane1-R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-11-09T01:09:58.874532+00:00",
"file_format": "fastq",
"file_size": 14236074765,
"href": "/sequence-files/IGVFFI2055FUEP/@@download/IGVFFI2055FUEP.fastq.gz",
"s3_uri": "s3://igvf-files/2023/11/09/5b37d5f6-12f7-43f9-b20d-fc28b54b7ba4/IGVFFI2055FUEP.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008637/",
"status": "released",
"term_name": "Illumina NovaSeq 6000"
},
"status": "released",
"submitted_file_name": "/data/reddylab/Alex/IGVF/data_submissions/raw_data/AIM_2_T_cell_project_1/GEX_CRISPRi_D3_S3_L001_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3515IWOR/",
"accession": "IGVFFI3515IWOR",
"aliases": [
"charles-gersbach:cd8-tcells-perturb-seq-crispri-gex-rep3-rep3-fastq-lane2-R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-11-09T01:16:46.385915+00:00",
"file_format": "fastq",
"file_size": 5680941224,
"href": "/sequence-files/IGVFFI3515IWOR/@@download/IGVFFI3515IWOR.fastq.gz",
"s3_uri": "s3://igvf-files/2023/11/09/4da79c66-96b7-4a2f-ac4e-b6b926f1a5a9/IGVFFI3515IWOR.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008637/",
"status": "released",
"term_name": "Illumina NovaSeq 6000"
},
"status": "released",
"submitted_file_name": "/data/reddylab/Alex/IGVF/data_submissions/raw_data/AIM_2_T_cell_project_1/GEX_CRISPRi_D3_S3_L002_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8510AXNZ/",
"accession": "IGVFFI8510AXNZ",
"aliases": [
"charles-gersbach:cd8-tcells-perturb-seq-crispri-gex-rep3-rep3-fastq-lane2-R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-11-09T01:19:30.897933+00:00",
"file_format": "fastq",
"file_size": 14155280312,
"href": "/sequence-files/IGVFFI8510AXNZ/@@download/IGVFFI8510AXNZ.fastq.gz",
"s3_uri": "s3://igvf-files/2023/11/09/8149ba25-0e0e-4369-878c-68cc84b278db/IGVFFI8510AXNZ.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008637/",
"status": "released",
"term_name": "Illumina NovaSeq 6000"
},
"status": "released",
"submitted_file_name": "/data/reddylab/Alex/IGVF/data_submissions/raw_data/AIM_2_T_cell_project_1/GEX_CRISPRi_D3_S3_L002_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8540PIGY/",
"accession": "IGVFFI8540PIGY",
"aliases": [
"charles-gersbach:cd8-tcells-perturb-seq-crispri-gex-rep3-rep3-fastq-lane3-R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-11-09T01:26:13.077684+00:00",
"file_format": "fastq",
"file_size": 5683642535,
"href": "/sequence-files/IGVFFI8540PIGY/@@download/IGVFFI8540PIGY.fastq.gz",
"s3_uri": "s3://igvf-files/2023/11/09/c7e2a27d-249b-4845-a064-f30b276326cb/IGVFFI8540PIGY.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008637/",
"status": "released",
"term_name": "Illumina NovaSeq 6000"
},
"status": "released",
"submitted_file_name": "/data/reddylab/Alex/IGVF/data_submissions/raw_data/AIM_2_T_cell_project_1/GEX_CRISPRi_D3_S3_L003_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0810KWLC/",
"accession": "IGVFFI0810KWLC",
"aliases": [
"charles-gersbach:cd8-tcells-perturb-seq-crispri-gex-rep3-rep3-fastq-lane3-R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-11-09T01:29:04.145027+00:00",
"file_format": "fastq",
"file_size": 14151736554,
"href": "/sequence-files/IGVFFI0810KWLC/@@download/IGVFFI0810KWLC.fastq.gz",
"s3_uri": "s3://igvf-files/2023/11/09/afff4447-7d3a-4f13-b491-76823991ccc6/IGVFFI0810KWLC.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008637/",
"status": "released",
"term_name": "Illumina NovaSeq 6000"
},
"status": "released",
"submitted_file_name": "/data/reddylab/Alex/IGVF/data_submissions/raw_data/AIM_2_T_cell_project_1/GEX_CRISPRi_D3_S3_L003_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6382YKWB/",
"accession": "IGVFFI6382YKWB",
"aliases": [
"charles-gersbach:cd8-tcells-perturb-seq-crispri-gex-rep3-rep3-fastq-lane4-R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-11-09T01:35:55.815745+00:00",
"file_format": "fastq",
"file_size": 5716966767,
"href": "/sequence-files/IGVFFI6382YKWB/@@download/IGVFFI6382YKWB.fastq.gz",
"s3_uri": "s3://igvf-files/2023/11/09/e0b63659-5070-48ee-b59d-ae983f97248e/IGVFFI6382YKWB.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008637/",
"status": "released",
"term_name": "Illumina NovaSeq 6000"
},
"status": "released",
"submitted_file_name": "/data/reddylab/Alex/IGVF/data_submissions/raw_data/AIM_2_T_cell_project_1/GEX_CRISPRi_D3_S3_L004_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0961HLAP/",
"accession": "IGVFFI0961HLAP",
"aliases": [
"charles-gersbach:cd8-tcells-perturb-seq-crispri-gex-rep3-rep3-fastq-lane4-R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-11-09T01:38:46.551581+00:00",
"file_format": "fastq",
"file_size": 14244238919,
"href": "/sequence-files/IGVFFI0961HLAP/@@download/IGVFFI0961HLAP.fastq.gz",
"s3_uri": "s3://igvf-files/2023/11/09/d6bfb12c-2dd1-430a-bce0-34954404900d/IGVFFI0961HLAP.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008637/",
"status": "released",
"term_name": "Illumina NovaSeq 6000"
},
"status": "released",
"submitted_file_name": "/data/reddylab/Alex/IGVF/data_submissions/raw_data/AIM_2_T_cell_project_1/GEX_CRISPRi_D3_S3_L004_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI1992VILF/",
"accession": "IGVFFI1992VILF",
"aliases": [
"charles-gersbach:cd8-tcells-perturb-seq-crispri-gex-rep3-rep3-fastq-lane1_seqspec"
],
"content_type": "seqspec",
"creation_timestamp": "2024-09-20T16:49:33.354998+00:00",
"file_format": "yaml",
"file_size": 981,
"href": "/configuration-files/IGVFFI1992VILF/@@download/IGVFFI1992VILF.yaml.gz",
"s3_uri": "s3://igvf-files/2024/09/20/0e3967f8-e1af-4313-b235-df324dca01ce/IGVFFI1992VILF.yaml.gz",
"status": "released",
"submitted_file_name": "/datacommons/gersbachlab/Ruhi/IGVFseqspec/CRISPRiD3_S3nS9_L001.rna.yaml.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI9664FBRY/",
"accession": "IGVFFI9664FBRY",
"aliases": [
"charles-gersbach:cd8-tcells-perturb-seq-crispri-gex-rep3-rep3-fastq-lane2_seqspec"
],
"content_type": "seqspec",
"creation_timestamp": "2024-09-20T16:49:35.935019+00:00",
"file_format": "yaml",
"file_size": 982,
"href": "/configuration-files/IGVFFI9664FBRY/@@download/IGVFFI9664FBRY.yaml.gz",
"s3_uri": "s3://igvf-files/2024/09/20/90af4e1f-3eec-4dde-838d-97a03d35cca3/IGVFFI9664FBRY.yaml.gz",
"status": "released",
"submitted_file_name": "/datacommons/gersbachlab/Ruhi/IGVFseqspec/CRISPRiD3_S3nS9_L002.rna.yaml.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI3361HIQA/",
"accession": "IGVFFI3361HIQA",
"aliases": [
"charles-gersbach:cd8-tcells-perturb-seq-crispri-gex-rep3-rep3-fastq-lane3_seqspec"
],
"content_type": "seqspec",
"creation_timestamp": "2024-09-20T16:49:38.844763+00:00",
"file_format": "yaml",
"file_size": 982,
"href": "/configuration-files/IGVFFI3361HIQA/@@download/IGVFFI3361HIQA.yaml.gz",
"s3_uri": "s3://igvf-files/2024/09/20/ba3ad3ae-9e48-4aa9-8d2b-25056861f636/IGVFFI3361HIQA.yaml.gz",
"status": "released",
"submitted_file_name": "/datacommons/gersbachlab/Ruhi/IGVFseqspec/CRISPRiD3_S3nS9_L003.rna.yaml.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI8015EHXD/",
"accession": "IGVFFI8015EHXD",
"aliases": [
"charles-gersbach:cd8-tcells-perturb-seq-crispri-gex-rep3-rep3-fastq-lane4_seqspec"
],
"content_type": "seqspec",
"creation_timestamp": "2024-09-20T16:49:40.595907+00:00",
"file_format": "yaml",
"file_size": 982,
"href": "/configuration-files/IGVFFI8015EHXD/@@download/IGVFFI8015EHXD.yaml.gz",
"s3_uri": "s3://igvf-files/2024/09/20/f877acdc-e4ec-403e-a961-3016a798b811/IGVFFI8015EHXD.yaml.gz",
"status": "released",
"submitted_file_name": "/datacommons/gersbachlab/Ruhi/IGVFseqspec/CRISPRiD3_S3nS9_L004.rna.yaml.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS9445RJOU/"
],
"lab": {
"@id": "/labs/charles-gersbach/",
"title": "Charles Gersbach, Duke"
},
"notes": "The readout 86015c12-b9a6-43ba-9601-5d75aab4d39c was removed from this measurement set. This file_set previously had f9e9ffe1-b463-4b15-964c-e926bfcf58a8 submitted as library_construction_platform, but the property library_construction_platform has been now removed. This measurement set previously used 5' to 3' as strand_specificity, but the strand_specificity has now been updated to 5 prime to 3 prime via an upgrade.",
"onlist_files": [
"/tabular-files/IGVFFI9487JPEN/"
],
"onlist_method": "no combination",
"preferred_assay_title": "Perturb-seq",
"protocols": [
"https://www.protocols.io/view/perturb-seq-characterizing-regulators-of-t-cell-fu-c5s9y6h6",
"https://www.protocols.io/view/crispri-tiling-screens-c5rby52n"
],
"publications": [
{
"@id": "/publications/6cc80a53-4ca1-4bd4-9942-f0f335b7ec20/",
"publication_identifiers": [
"PMID:37945901",
"doi:10.1038/s41588-023-01554-0",
"PMCID:PMC10703699"
],
"status": "released"
}
],
"release_timestamp": "2024-10-18T19:50:07.271031+00:00",
"samples": [
{
"@id": "/primary-cells/IGVFSM5189UBOI/",
"@type": [
"PrimaryCell",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM5189UBOI",
"aliases": [
"charles-gersbach:cd8-tcells-primary-cell-crispri-rep3"
],
"classifications": [
"primary cell"
],
"institutional_certificates": [],
"modifications": [
{
"@id": "/crispr-modifications/95393c9a-637d-43f6-baf9-662e45d28d61/",
"modality": "interference",
"status": "released"
}
],
"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": "Homo sapiens CD8-positive, alpha-beta memory T cell modified with CRISPRi Sa-dCas9-KOX1-KRAB, transduced (lentivirus) with a guide library (MOI of 0.4)",
"taxa": "Homo sapiens"
}
],
"schema_version": "26",
"status": "released",
"strand_specificity": "5 prime to 3 prime",
"submitted_by": {
"@id": "/users/29f5f78d-ac90-421e-90c6-a90e1dc407a7/",
"title": "Alejandro Barrera"
},
"submitted_files_timestamp": "2023-11-09T01:07:05.239635+00:00",
"summary": "CRISPR interference Perturb-seq integrating a guide (sgRNA) library targeting transcription start sites in 24 genes",
"uuid": "7834c361-d558-42d5-98a1-91b2219b3c30"
}