{
"@context": "/terms/",
"@id": "/analysis-sets/IGVFDS5498STRV/",
"@type": [
"AnalysisSet",
"FileSet",
"Item"
],
"accession": "IGVFDS5498STRV",
"aliases": [
"charles-gersbach:cd8-tcells-intermediate-analysis-crispri-cd2"
],
"assay_titles": [
"CRISPR FACS screen"
],
"audit": {
"INTERNAL_ACTION": [
{
"category": "mismatched status",
"detail": "Released alignment file [IGVFFI8487IOGJ](/alignment-files/IGVFFI8487IOGJ/) has in progress subobject reference file [IGVFFI8884FZOC](/reference-files/IGVFFI8884FZOC/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/alignment-files/IGVFFI8487IOGJ/"
},
{
"category": "mismatched status",
"detail": "Released alignment file [IGVFFI2317FRUV](/alignment-files/IGVFFI2317FRUV/) has in progress subobject reference file [IGVFFI8884FZOC](/reference-files/IGVFFI8884FZOC/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/alignment-files/IGVFFI2317FRUV/"
},
{
"category": "mismatched status",
"detail": "Released alignment file [IGVFFI6108ZPCY](/alignment-files/IGVFFI6108ZPCY/) has in progress subobject reference file [IGVFFI8884FZOC](/reference-files/IGVFFI8884FZOC/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/alignment-files/IGVFFI6108ZPCY/"
},
{
"category": "mismatched status",
"detail": "Released alignment file [IGVFFI8774OGSY](/alignment-files/IGVFFI8774OGSY/) has in progress subobject reference file [IGVFFI8884FZOC](/reference-files/IGVFFI8884FZOC/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/alignment-files/IGVFFI8774OGSY/"
}
],
"WARNING": [
{
"category": "missing age",
"detail": "Primary cell [IGVFSM6350DJQS](/primary-cells/IGVFSM6350DJQS/) 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/IGVFSM6350DJQS/"
},
{
"category": "missing age",
"detail": "Primary cell [IGVFSM7658WDNM](/primary-cells/IGVFSM7658WDNM/) 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/IGVFSM7658WDNM/"
},
{
"category": "missing age",
"detail": "Primary cell [IGVFSM7030KVXG](/primary-cells/IGVFSM7030KVXG/) 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/IGVFSM7030KVXG/"
},
{
"category": "missing age",
"detail": "Primary cell [IGVFSM4694MBIW](/primary-cells/IGVFSM4694MBIW/) 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/IGVFSM4694MBIW/"
}
]
},
"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": "2024-09-20T15:06:17.479430+00:00",
"donors": [
{
"@id": "/human-donors/IGVFDO4080HFHD/",
"accession": "IGVFDO4080HFHD",
"aliases": [
"charles-gersbach:cd8-tcells-donor-15"
],
"sex": "unspecified",
"status": "released",
"taxa": "Homo sapiens"
},
{
"@id": "/human-donors/IGVFDO1423VLXL/",
"accession": "IGVFDO1423VLXL",
"aliases": [
"charles-gersbach:cd8-tcells-donor-16"
],
"sex": "unspecified",
"status": "released",
"taxa": "Homo sapiens"
}
],
"file_set_type": "intermediate analysis",
"files": [
{
"@id": "/alignment-files/IGVFFI6108ZPCY/",
"accession": "IGVFFI6108ZPCY",
"aliases": [
"charles-gersbach:cd8-tcells-alignment-crispri-cd2-low-bin-rep3"
],
"assembly": "custom",
"content_type": "alignments",
"creation_timestamp": "2024-10-15T18:49:19.383362+00:00",
"file_format": "bam",
"file_size": 23942994,
"href": "/alignment-files/IGVFFI6108ZPCY/@@download/IGVFFI6108ZPCY.bam",
"s3_uri": "s3://igvf-files/2024/10/15/ae04d091-bd5f-4756-b871-cbfe8abb4077/IGVFFI6108ZPCY.bam",
"submitted_file_name": "/data/reddylab/Alex/IGVF/data_submissions/processed_data/AIM_2_T_cell_project_1/pSM8-Low-R3_S16.sorted.bam",
"upload_status": "validated"
},
{
"@id": "/alignment-files/IGVFFI8774OGSY/",
"accession": "IGVFFI8774OGSY",
"aliases": [
"charles-gersbach:cd8-tcells-alignment-crispri-cd2-low-bin-rep2"
],
"assembly": "custom",
"content_type": "alignments",
"creation_timestamp": "2024-10-15T18:48:35.603818+00:00",
"file_format": "bam",
"file_size": 18935493,
"href": "/alignment-files/IGVFFI8774OGSY/@@download/IGVFFI8774OGSY.bam",
"s3_uri": "s3://igvf-files/2024/10/15/41bec344-a5a6-41ee-a756-01285d827826/IGVFFI8774OGSY.bam",
"submitted_file_name": "/data/reddylab/Alex/IGVF/data_submissions/processed_data/AIM_2_T_cell_project_1/pSM8-Low-R2_S13.sorted.bam",
"upload_status": "validated"
},
{
"@id": "/alignment-files/IGVFFI8487IOGJ/",
"accession": "IGVFFI8487IOGJ",
"aliases": [
"charles-gersbach:cd8-tcells-alignment-crispri-cd2-high-bin-rep3"
],
"assembly": "custom",
"content_type": "alignments",
"creation_timestamp": "2024-10-15T18:51:36.445412+00:00",
"file_format": "bam",
"file_size": 20791936,
"href": "/alignment-files/IGVFFI8487IOGJ/@@download/IGVFFI8487IOGJ.bam",
"s3_uri": "s3://igvf-files/2024/10/15/9491b447-2a0a-4429-b01a-3251c142abe4/IGVFFI8487IOGJ.bam",
"submitted_file_name": "/data/reddylab/Alex/IGVF/data_submissions/processed_data/AIM_2_T_cell_project_1/pSM8-High-R3_S17.sorted.bam",
"upload_status": "validated"
},
{
"@id": "/alignment-files/IGVFFI2317FRUV/",
"accession": "IGVFFI2317FRUV",
"aliases": [
"charles-gersbach:cd8-tcells-alignment-crispri-cd2-high-bin-rep2"
],
"assembly": "custom",
"content_type": "alignments",
"creation_timestamp": "2024-10-15T18:51:12.190814+00:00",
"file_format": "bam",
"file_size": 20932549,
"href": "/alignment-files/IGVFFI2317FRUV/@@download/IGVFFI2317FRUV.bam",
"s3_uri": "s3://igvf-files/2024/10/15/8c23197c-10cf-4e87-9de0-d00f0cf35f91/IGVFFI2317FRUV.bam",
"submitted_file_name": "/data/reddylab/Alex/IGVF/data_submissions/processed_data/AIM_2_T_cell_project_1/pSM8-High-R2_S14.sorted.bam",
"upload_status": "validated"
}
],
"functional_assay_mechanisms": [],
"input_file_sets": [
{
"@id": "/auxiliary-sets/IGVFDS0506WOIW/",
"accession": "IGVFDS0506WOIW",
"aliases": [
"charles-gersbach:cd8-tcells-auxiliary-set-crispri-cd2-low-bin-rep2"
],
"file_set_type": "gRNA sequencing"
},
{
"@id": "/auxiliary-sets/IGVFDS7413JPIS/",
"accession": "IGVFDS7413JPIS",
"aliases": [
"charles-gersbach:cd8-tcells-auxiliary-set-crispri-cd2-low-bin-rep3"
],
"file_set_type": "gRNA sequencing"
},
{
"@id": "/auxiliary-sets/IGVFDS8866USWP/",
"accession": "IGVFDS8866USWP",
"aliases": [
"charles-gersbach:cd8-tcells-auxiliary-set-crispri-cd2-high-bin-rep2"
],
"file_set_type": "gRNA sequencing"
},
{
"@id": "/auxiliary-sets/IGVFDS8876GCAP/",
"accession": "IGVFDS8876GCAP",
"aliases": [
"charles-gersbach:cd8-tcells-auxiliary-set-crispri-cd2-high-bin-rep3"
],
"file_set_type": "gRNA sequencing"
}
],
"input_for": [
"/analysis-sets/IGVFDS5157TBYH/"
],
"lab": {
"@id": "/labs/charles-gersbach/",
"title": "Charles Gersbach, Duke"
},
"protocols": [],
"publications": [
{
"@id": "/publications/6cc80a53-4ca1-4bd4-9942-f0f335b7ec20/",
"publication_identifiers": [
"PMID:37945901",
"doi:10.1038/s41588-023-01554-0",
"PMCID:PMC10703699"
]
}
],
"release_timestamp": "2024-11-18T21:09:03.175947+00:00",
"sample_summary": "CD8-positive, alpha-beta memory T cell primary cell, modified with CRISPR modifications, transfected with a guide library, sorted on expression of CD2",
"samples": [
{
"@id": "/primary-cells/IGVFSM4694MBIW/",
"@type": [
"PrimaryCell",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM4694MBIW",
"aliases": [
"charles-gersbach:cd8-tcells-primary-cell-crispri-cd2-low-bin-rep2"
],
"classifications": [
"primary cell"
],
"construct_library_sets": [
"/construct-library-sets/IGVFDS8345ZMZW/"
],
"modifications": [
{
"@id": "/crispr-modifications/95393c9a-637d-43f6-baf9-662e45d28d61/",
"modality": "interference"
}
],
"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 (sorting details: FACS bin for 0-10% expression of CD2 ) modified with CRISPRi Sa-dCas9, transduced (lentivirus) with a guide library (MOI of 0.4)",
"taxa": "Homo sapiens"
},
{
"@id": "/primary-cells/IGVFSM6350DJQS/",
"@type": [
"PrimaryCell",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM6350DJQS",
"aliases": [
"charles-gersbach:cd8-tcells-primary-cell-crispri-cd2-low-bin-rep3"
],
"classifications": [
"primary cell"
],
"construct_library_sets": [
"/construct-library-sets/IGVFDS8345ZMZW/"
],
"modifications": [
{
"@id": "/crispr-modifications/95393c9a-637d-43f6-baf9-662e45d28d61/",
"modality": "interference"
}
],
"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 (sorting details: FACS bin for 0-10% expression of CD2) modified with CRISPRi Sa-dCas9, transduced (lentivirus) with a guide library (MOI of 0.4)",
"taxa": "Homo sapiens"
},
{
"@id": "/primary-cells/IGVFSM7658WDNM/",
"@type": [
"PrimaryCell",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM7658WDNM",
"aliases": [
"charles-gersbach:cd8-tcells-primary-cell-crispri-cd2-high-bin-rep2"
],
"classifications": [
"primary cell"
],
"construct_library_sets": [
"/construct-library-sets/IGVFDS8345ZMZW/"
],
"modifications": [
{
"@id": "/crispr-modifications/95393c9a-637d-43f6-baf9-662e45d28d61/",
"modality": "interference"
}
],
"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 (sorting details: FACS bin for 90-100% expression of CD2 ) modified with CRISPRi Sa-dCas9, transduced (lentivirus) with a guide library (MOI of 0.4)",
"taxa": "Homo sapiens"
},
{
"@id": "/primary-cells/IGVFSM7030KVXG/",
"@type": [
"PrimaryCell",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM7030KVXG",
"aliases": [
"charles-gersbach:cd8-tcells-primary-cell-crispri-cd2-high-bin-rep3"
],
"classifications": [
"primary cell"
],
"construct_library_sets": [
"/construct-library-sets/IGVFDS8345ZMZW/"
],
"modifications": [
{
"@id": "/crispr-modifications/95393c9a-637d-43f6-baf9-662e45d28d61/",
"modality": "interference"
}
],
"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 (sorting details: FACS bin for 90-100% expression of CD2) modified with CRISPRi Sa-dCas9, transduced (lentivirus) with a guide library (MOI of 0.4)",
"taxa": "Homo sapiens"
}
],
"schema_version": "9",
"status": "released",
"submitted_by": {
"@id": "/users/29f5f78d-ac90-421e-90c6-a90e1dc407a7/",
"title": "Alejandro Barrera"
},
"submitted_files_timestamp": "2024-10-15T18:48:35.603818+00:00",
"summary": "CRISPR interference FACS screen targeting CD2: alignments",
"uuid": "baeb521d-0294-4610-9bef-b4d4aba46622",
"workflows": [
{
"@id": "/workflows/IGVFWF8837BHJV/",
"accession": "IGVFWF8837BHJV",
"name": "Gersbach FACS CRISPR screen workflow"
}
]
}