{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS1333MBPK/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS1333MBPK",
"aliases": [
"charles-gersbach:cd8-tcells-perturb-seq-crispri-gex-rep2"
],
"assay_term": {
"@id": "/assay-terms/OBI_0003660/",
"status": "released",
"term_name": "in vitro CRISPR screen using single-cell RNA-seq"
},
"audit": {
"WARNING": [
{
"category": "missing age",
"detail": "Primary cell [IGVFSM2747RJFY](/primary-cells/IGVFSM2747RJFY/) 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/IGVFSM2747RJFY/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS2399UCGA/",
"accession": "IGVFDS2399UCGA",
"aliases": [
"charles-gersbach:cd8-tcells-perturb-seq-crispri-grna-rep2"
],
"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"
},
"control_for": [],
"creation_timestamp": "2023-11-08T19:33:40.926197+00:00",
"donors": [
{
"@id": "/human-donors/IGVFDO6082RNLT/",
"accession": "IGVFDO6082RNLT",
"aliases": [
"charles-gersbach:cd8-tcells-donor-7"
],
"sex": "unspecified",
"status": "released",
"taxa": "Homo sapiens"
}
],
"externally_hosted": false,
"file_set_type": "experimental data",
"files": [
{
"@id": "/sequence-files/IGVFFI7428GSBY/",
"accession": "IGVFFI7428GSBY",
"aliases": [
"charles-gersbach:cd8-tcells-perturb-seq-crispri-gex-rep2-rep2-fastq-lane2-R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-11-09T00:36:24.753511+00:00",
"file_format": "fastq",
"file_size": 16503370691,
"href": "/sequence-files/IGVFFI7428GSBY/@@download/IGVFFI7428GSBY.fastq.gz",
"s3_uri": "s3://igvf-files/2023/11/09/2c041f01-df53-4bad-ad4f-9aea6caa83f4/IGVFFI7428GSBY.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_D2_S2_L002_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8844XDHB/",
"accession": "IGVFFI8844XDHB",
"aliases": [
"charles-gersbach:cd8-tcells-perturb-seq-crispri-gex-rep2-rep2-fastq-lane4-R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-11-09T00:58:58.522085+00:00",
"file_format": "fastq",
"file_size": 16585762033,
"href": "/sequence-files/IGVFFI8844XDHB/@@download/IGVFFI8844XDHB.fastq.gz",
"s3_uri": "s3://igvf-files/2023/11/09/1a315190-5ef2-4e07-864b-4dab95744bbe/IGVFFI8844XDHB.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_D2_S2_L004_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5242KCVA/",
"accession": "IGVFFI5242KCVA",
"aliases": [
"charles-gersbach:cd8-tcells-perturb-seq-crispri-gex-rep2-rep2-fastq-lane1-R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-11-09T00:25:01.014954+00:00",
"file_format": "fastq",
"file_size": 16548894569,
"href": "/sequence-files/IGVFFI5242KCVA/@@download/IGVFFI5242KCVA.fastq.gz",
"s3_uri": "s3://igvf-files/2023/11/09/726751a5-fd56-49df-a28e-069cc0f12d28/IGVFFI5242KCVA.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_D2_S2_L001_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7143SLWN/",
"accession": "IGVFFI7143SLWN",
"aliases": [
"charles-gersbach:cd8-tcells-perturb-seq-crispri-gex-rep2-rep2-fastq-lane3-R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-11-09T00:47:38.160742+00:00",
"file_format": "fastq",
"file_size": 16428824769,
"href": "/sequence-files/IGVFFI7143SLWN/@@download/IGVFFI7143SLWN.fastq.gz",
"s3_uri": "s3://igvf-files/2023/11/09/b51ad711-8b5e-4fc5-9ed3-7ad3278d4097/IGVFFI7143SLWN.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_D2_S2_L003_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4978WOQZ/",
"accession": "IGVFFI4978WOQZ",
"aliases": [
"charles-gersbach:cd8-tcells-perturb-seq-crispri-gex-rep2-rep2-fastq-lane2-R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-11-09T00:33:05.349493+00:00",
"file_format": "fastq",
"file_size": 6608033322,
"href": "/sequence-files/IGVFFI4978WOQZ/@@download/IGVFFI4978WOQZ.fastq.gz",
"s3_uri": "s3://igvf-files/2023/11/09/d2f09024-8476-40f5-9757-e018143f197b/IGVFFI4978WOQZ.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_D2_S2_L002_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1785SEVE/",
"accession": "IGVFFI1785SEVE",
"aliases": [
"charles-gersbach:cd8-tcells-perturb-seq-crispri-gex-rep2-rep2-fastq-lane4-R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-11-09T00:55:36.893420+00:00",
"file_format": "fastq",
"file_size": 6642737910,
"href": "/sequence-files/IGVFFI1785SEVE/@@download/IGVFFI1785SEVE.fastq.gz",
"s3_uri": "s3://igvf-files/2023/11/09/ad507c8d-989c-4df9-a660-489a3a1859ce/IGVFFI1785SEVE.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_D2_S2_L004_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2557GAGA/",
"accession": "IGVFFI2557GAGA",
"aliases": [
"charles-gersbach:cd8-tcells-perturb-seq-crispri-gex-rep2-rep2-fastq-lane1-R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-11-09T00:21:47.944313+00:00",
"file_format": "fastq",
"file_size": 6620942472,
"href": "/sequence-files/IGVFFI2557GAGA/@@download/IGVFFI2557GAGA.fastq.gz",
"s3_uri": "s3://igvf-files/2023/11/09/8f7bf43a-cfe1-4233-aa15-a2767d997a85/IGVFFI2557GAGA.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_D2_S2_L001_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0258POJN/",
"accession": "IGVFFI0258POJN",
"aliases": [
"charles-gersbach:cd8-tcells-perturb-seq-crispri-gex-rep2-rep2-fastq-lane3-R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-11-09T00:44:22.878996+00:00",
"file_format": "fastq",
"file_size": 6585713995,
"href": "/sequence-files/IGVFFI0258POJN/@@download/IGVFFI0258POJN.fastq.gz",
"s3_uri": "s3://igvf-files/2023/11/09/3df51864-58af-4180-8661-65b54651080a/IGVFFI0258POJN.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_D2_S2_L003_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI1478KFQX/",
"accession": "IGVFFI1478KFQX",
"aliases": [
"charles-gersbach:cd8-tcells-perturb-seq-crispri-gex-rep2-rep2-fastq-lane4_seqspec"
],
"content_type": "seqspec",
"creation_timestamp": "2024-09-20T16:49:30.540004+00:00",
"file_format": "yaml",
"file_size": 983,
"href": "/configuration-files/IGVFFI1478KFQX/@@download/IGVFFI1478KFQX.yaml.gz",
"s3_uri": "s3://igvf-files/2024/09/20/1b433a5d-982d-4697-b441-cb4ca2eaf425/IGVFFI1478KFQX.yaml.gz",
"status": "released",
"submitted_file_name": "/datacommons/gersbachlab/Ruhi/IGVFseqspec/CRISPRiD2_S2nS8_L004.rna.yaml.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI2184ODYQ/",
"accession": "IGVFFI2184ODYQ",
"aliases": [
"charles-gersbach:cd8-tcells-perturb-seq-crispri-gex-rep2-rep2-fastq-lane1_seqspec"
],
"content_type": "seqspec",
"creation_timestamp": "2024-09-20T16:49:24.115120+00:00",
"file_format": "yaml",
"file_size": 982,
"href": "/configuration-files/IGVFFI2184ODYQ/@@download/IGVFFI2184ODYQ.yaml.gz",
"s3_uri": "s3://igvf-files/2024/09/20/ca32ed31-f88f-4233-848c-a9500740947a/IGVFFI2184ODYQ.yaml.gz",
"status": "released",
"submitted_file_name": "/datacommons/gersbachlab/Ruhi/IGVFseqspec/CRISPRiD2_S2nS8_L001.rna.yaml.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI5529AHMN/",
"accession": "IGVFFI5529AHMN",
"aliases": [
"charles-gersbach:cd8-tcells-perturb-seq-crispri-gex-rep2-rep2-fastq-lane3_seqspec"
],
"content_type": "seqspec",
"creation_timestamp": "2024-09-20T16:49:28.367800+00:00",
"file_format": "yaml",
"file_size": 983,
"href": "/configuration-files/IGVFFI5529AHMN/@@download/IGVFFI5529AHMN.yaml.gz",
"s3_uri": "s3://igvf-files/2024/09/20/aa111843-8415-48f1-b705-d0bea9f12452/IGVFFI5529AHMN.yaml.gz",
"status": "released",
"submitted_file_name": "/datacommons/gersbachlab/Ruhi/IGVFseqspec/CRISPRiD2_S2nS8_L003.rna.yaml.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI1013CBJR/",
"accession": "IGVFFI1013CBJR",
"aliases": [
"charles-gersbach:cd8-tcells-perturb-seq-crispri-gex-rep2-rep2-fastq-lane2_seqspec"
],
"content_type": "seqspec",
"creation_timestamp": "2024-09-20T16:49:26.276225+00:00",
"file_format": "yaml",
"file_size": 983,
"href": "/configuration-files/IGVFFI1013CBJR/@@download/IGVFFI1013CBJR.yaml.gz",
"s3_uri": "s3://igvf-files/2024/09/20/645d67f1-1efe-4fe9-933d-114c98b76ce0/IGVFFI1013CBJR.yaml.gz",
"status": "released",
"submitted_file_name": "/datacommons/gersbachlab/Ruhi/IGVFseqspec/CRISPRiD2_S2nS8_L002.rna.yaml.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS3319RFFN/"
],
"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.",
"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": "2024-10-18T19:50:08.076446+00:00",
"samples": [
{
"@id": "/primary-cells/IGVFSM2747RJFY/",
"@type": [
"PrimaryCell",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM2747RJFY",
"aliases": [
"charles-gersbach:cd8-tcells-primary-cell-crispri-rep2"
],
"classifications": [
"primary cell"
],
"construct_library_sets": [
{
"@id": "/construct-library-sets/IGVFDS0821YMMV/",
"accession": "IGVFDS0821YMMV",
"file_set_type": "guide library",
"small_scale_gene_list": [
{
"@id": "/genes/ENSG00000156127/",
"geneid": "ENSG00000156127",
"name": "basic leucine zipper ATF-like transcription factor",
"status": "released",
"summary": "BATF - ENSG00000156127 (Homo sapiens)",
"symbol": "BATF"
},
{
"@id": "/genes/ENSG00000123685/",
"geneid": "ENSG00000123685",
"name": "basic leucine zipper ATF-like transcription factor 3",
"status": "released",
"summary": "BATF3 - ENSG00000123685 (Homo sapiens)",
"symbol": "BATF3"
},
{
"@id": "/genes/ENSG00000134107/",
"geneid": "ENSG00000134107",
"name": "basic helix-loop-helix family member e40",
"status": "released",
"summary": "BHLHE40 - ENSG00000134107 (Homo sapiens)",
"symbol": "BHLHE40"
},
{
"@id": "/genes/ENSG00000095794/",
"geneid": "ENSG00000095794",
"name": "cAMP responsive element modulator",
"status": "released",
"summary": "CREM - ENSG00000095794 (Homo sapiens)",
"symbol": "CREM"
},
{
"@id": "/genes/ENSG00000163508/",
"geneid": "ENSG00000163508",
"name": "eomesodermin",
"status": "released",
"summary": "EOMES - ENSG00000163508 (Homo sapiens)",
"symbol": "EOMES"
},
{
"@id": "/genes/ENSG00000151702/",
"geneid": "ENSG00000151702",
"name": "Fli-1 proto-oncogene, ETS transcription factor",
"status": "released",
"summary": "FLI1 - ENSG00000151702 (Homo sapiens)",
"symbol": "FLI1"
},
{
"@id": "/genes/ENSG00000186564/",
"geneid": "ENSG00000186564",
"name": "forkhead box D2",
"status": "released",
"summary": "FOXD2 - ENSG00000186564 (Homo sapiens)",
"symbol": "FOXD2"
},
{
"@id": "/genes/ENSG00000150907/",
"geneid": "ENSG00000150907",
"name": "forkhead box O1",
"status": "released",
"summary": "FOXO1 - ENSG00000150907 (Homo sapiens)",
"symbol": "FOXO1"
},
{
"@id": "/genes/ENSG00000154727/",
"geneid": "ENSG00000154727",
"name": "GA binding protein transcription factor subunit alpha",
"status": "released",
"summary": "GABPA - ENSG00000154727 (Homo sapiens)",
"symbol": "GABPA"
},
{
"@id": "/genes/ENSG00000177374/",
"geneid": "ENSG00000177374",
"name": "HIC ZBTB transcriptional repressor 1",
"status": "released",
"summary": "HIC1 - ENSG00000177374 (Homo sapiens)",
"symbol": "HIC1"
},
{
"@id": "/genes/ENSG00000168310/",
"geneid": "ENSG00000168310",
"name": "interferon regulatory factor 2",
"status": "released",
"summary": "IRF2 - ENSG00000168310 (Homo sapiens)",
"symbol": "IRF2"
},
{
"@id": "/genes/ENSG00000177606/",
"geneid": "ENSG00000177606",
"name": "Jun proto-oncogene, AP-1 transcription factor subunit",
"status": "released",
"summary": "JUN - ENSG00000177606 (Homo sapiens)",
"symbol": "JUN"
},
{
"@id": "/genes/ENSG00000118513/",
"geneid": "ENSG00000118513",
"name": "MYB proto-oncogene, transcription factor",
"status": "released",
"summary": "MYB - ENSG00000118513 (Homo sapiens)",
"symbol": "MYB"
},
{
"@id": "/genes/ENSG00000072736/",
"geneid": "ENSG00000072736",
"name": "nuclear factor of activated T cells 3",
"status": "released",
"summary": "NFATC3 - ENSG00000072736 (Homo sapiens)",
"symbol": "NFATC3"
},
{
"@id": "/genes/ENSG00000082641/",
"geneid": "ENSG00000082641",
"name": "NFE2 like bZIP transcription factor 1",
"status": "released",
"summary": "NFE2L1 - ENSG00000082641 (Homo sapiens)",
"symbol": "NFE2L1"
},
{
"@id": "/genes/ENSG00000126368/",
"geneid": "ENSG00000126368",
"name": "nuclear receptor subfamily 1 group D member 1",
"status": "released",
"summary": "NR1D1 - ENSG00000126368 (Homo sapiens)",
"symbol": "NR1D1"
},
{
"@id": "/genes/ENSG00000123358/",
"geneid": "ENSG00000123358",
"name": "nuclear receptor subfamily 4 group A member 1",
"status": "released",
"summary": "NR4A1 - ENSG00000123358 (Homo sapiens)",
"symbol": "NR4A1"
},
{
"@id": "/genes/ENSG00000143190/",
"geneid": "ENSG00000143190",
"name": "POU class 2 homeobox 1",
"status": "released",
"summary": "POU2F1 - ENSG00000143190 (Homo sapiens)",
"symbol": "POU2F1"
},
{
"@id": "/genes/ENSG00000124782/",
"geneid": "ENSG00000124782",
"name": "ras responsive element binding protein 1",
"status": "released",
"summary": "RREB1 - ENSG00000124782 (Homo sapiens)",
"symbol": "RREB1"
},
{
"@id": "/genes/ENSG00000152284/",
"geneid": "ENSG00000152284",
"name": "transcription factor 7 like 1",
"status": "released",
"summary": "TCF7L1 - ENSG00000152284 (Homo sapiens)",
"symbol": "TCF7L1"
},
{
"@id": "/genes/ENSG00000184517/",
"geneid": "ENSG00000184517",
"name": "ZFP1 zinc finger protein",
"status": "released",
"summary": "ZFP1 - ENSG00000184517 (Homo sapiens)",
"symbol": "ZFP1"
},
{
"@id": "/genes/ENSG00000112182/",
"geneid": "ENSG00000112182",
"name": "BTB domain and CNC homolog 2",
"status": "released",
"summary": "BACH2 - ENSG00000112182 (Homo sapiens)",
"symbol": "BACH2"
},
{
"@id": "/genes/ENSG00000127528/",
"geneid": "ENSG00000127528",
"name": "KLF transcription factor 2",
"status": "released",
"summary": "KLF2 - ENSG00000127528 (Homo sapiens)",
"symbol": "KLF2"
},
{
"@id": "/genes/ENSG00000130816/",
"geneid": "ENSG00000130816",
"name": "DNA methyltransferase 1",
"status": "released",
"summary": "DNMT1 - ENSG00000130816 (Homo sapiens)",
"symbol": "DNMT1"
}
],
"status": "released",
"summary": "guide (sgRNA) library targeting transcription start sites in 24 genes"
}
],
"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": "CD8-positive, alpha-beta memory T cell, Homo sapiens modified with CRISPRi Sa-dCas9, transduced (lentivirus) with a guide library (MOI of 0.4)",
"taxa": "Homo sapiens"
}
],
"schema_version": "23",
"status": "released",
"submitted_by": {
"@id": "/users/29f5f78d-ac90-421e-90c6-a90e1dc407a7/",
"title": "Alejandro Barrera"
},
"submitted_files_timestamp": "2023-11-09T00:21:47.944313+00:00",
"summary": "CRISPR interference Perturb-seq integrating a guide (sgRNA) library targeting transcription start sites in 24 genes",
"uuid": "040e6129-fefb-467d-a0fe-75075e3c335e"
}