{
"@context": "/terms/",
"@id": "/analysis-sets/IGVFDS2716FVEL/",
"@type": [
"AnalysisSet",
"FileSet",
"Item"
],
"accession": "IGVFDS2716FVEL",
"aliases": [
"charles-gersbach:cd8-tcells-intermediate-analysis-crispri-b2m"
],
"assay_titles": [
"CRISPR FACS screen"
],
"audit": {
"INTERNAL_ACTION": [
{
"category": "mismatched status",
"detail": "Released alignment file [IGVFFI0916WHTV](/alignment-files/IGVFFI0916WHTV/) has in progress subobject reference file [IGVFFI9036JJXB](/reference-files/IGVFFI9036JJXB/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/alignment-files/IGVFFI0916WHTV/"
},
{
"category": "mismatched status",
"detail": "Released alignment file [IGVFFI2031KMAC](/alignment-files/IGVFFI2031KMAC/) has in progress subobject reference file [IGVFFI9036JJXB](/reference-files/IGVFFI9036JJXB/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/alignment-files/IGVFFI2031KMAC/"
},
{
"category": "mismatched status",
"detail": "Released alignment file [IGVFFI4242DKSL](/alignment-files/IGVFFI4242DKSL/) has in progress subobject reference file [IGVFFI9036JJXB](/reference-files/IGVFFI9036JJXB/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/alignment-files/IGVFFI4242DKSL/"
},
{
"category": "mismatched status",
"detail": "Released alignment file [IGVFFI3434RUJF](/alignment-files/IGVFFI3434RUJF/) has in progress subobject reference file [IGVFFI9036JJXB](/reference-files/IGVFFI9036JJXB/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/alignment-files/IGVFFI3434RUJF/"
},
{
"category": "mismatched status",
"detail": "Released alignment file [IGVFFI9063WAUS](/alignment-files/IGVFFI9063WAUS/) has in progress subobject reference file [IGVFFI9036JJXB](/reference-files/IGVFFI9036JJXB/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/alignment-files/IGVFFI9063WAUS/"
},
{
"category": "mismatched status",
"detail": "Released alignment file [IGVFFI5903FMQU](/alignment-files/IGVFFI5903FMQU/) has in progress subobject reference file [IGVFFI9036JJXB](/reference-files/IGVFFI9036JJXB/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/alignment-files/IGVFFI5903FMQU/"
}
],
"WARNING": [
{
"category": "missing age",
"detail": "Primary cell [IGVFSM1190UUKW](/primary-cells/IGVFSM1190UUKW/) 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/IGVFSM1190UUKW/"
},
{
"category": "missing age",
"detail": "Primary cell [IGVFSM3073WHFV](/primary-cells/IGVFSM3073WHFV/) 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/IGVFSM3073WHFV/"
},
{
"category": "missing age",
"detail": "Primary cell [IGVFSM6062UNTJ](/primary-cells/IGVFSM6062UNTJ/) 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/IGVFSM6062UNTJ/"
},
{
"category": "missing age",
"detail": "Primary cell [IGVFSM7452ZWAU](/primary-cells/IGVFSM7452ZWAU/) 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/IGVFSM7452ZWAU/"
},
{
"category": "missing age",
"detail": "Primary cell [IGVFSM3427LEEW](/primary-cells/IGVFSM3427LEEW/) 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/IGVFSM3427LEEW/"
},
{
"category": "missing age",
"detail": "Primary cell [IGVFSM4508IIAY](/primary-cells/IGVFSM4508IIAY/) 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/IGVFSM4508IIAY/"
}
]
},
"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": "2024-09-20T15:06:19.145061+00:00",
"donors": [
{
"@id": "/human-donors/IGVFDO3455VIHN/",
"accession": "IGVFDO3455VIHN",
"aliases": [
"charles-gersbach:cd8-tcells-donor-19"
],
"sex": "unspecified",
"status": "released",
"taxa": "Homo sapiens"
},
{
"@id": "/human-donors/IGVFDO4200TDAP/",
"accession": "IGVFDO4200TDAP",
"aliases": [
"charles-gersbach:cd8-tcells-donor-18"
],
"sex": "unspecified",
"status": "released",
"taxa": "Homo sapiens"
},
{
"@id": "/human-donors/IGVFDO8199EHWU/",
"accession": "IGVFDO8199EHWU",
"aliases": [
"charles-gersbach:cd8-tcells-donor-17"
],
"sex": "unspecified",
"status": "released",
"taxa": "Homo sapiens"
}
],
"file_set_type": "intermediate analysis",
"files": [
{
"@id": "/alignment-files/IGVFFI9063WAUS/",
"accession": "IGVFFI9063WAUS",
"aliases": [
"charles-gersbach:cd8-tcells-alignment-crispri-b2m-low-bin-rep2"
],
"assembly": "custom",
"content_type": "alignments",
"creation_timestamp": "2024-10-15T18:50:18.526743+00:00",
"file_format": "bam",
"file_size": 5079219,
"href": "/alignment-files/IGVFFI9063WAUS/@@download/IGVFFI9063WAUS.bam",
"s3_uri": "s3://igvf-files/2024/10/15/e043fe1f-f389-4cd6-b3b5-ebc28f7429fd/IGVFFI9063WAUS.bam",
"submitted_file_name": "/data/reddylab/Alex/IGVF/data_submissions/processed_data/AIM_2_T_cell_project_1/B2M-Low-R2_S7.sorted.bam",
"upload_status": "validated"
},
{
"@id": "/alignment-files/IGVFFI4242DKSL/",
"accession": "IGVFFI4242DKSL",
"aliases": [
"charles-gersbach:cd8-tcells-alignment-crispri-b2m-high-bin-rep2"
],
"assembly": "custom",
"content_type": "alignments",
"creation_timestamp": "2024-10-15T18:52:40.653370+00:00",
"file_format": "bam",
"file_size": 16445235,
"href": "/alignment-files/IGVFFI4242DKSL/@@download/IGVFFI4242DKSL.bam",
"s3_uri": "s3://igvf-files/2024/10/15/b5ef1cc3-392b-4056-af6b-b5ba5853cacd/IGVFFI4242DKSL.bam",
"submitted_file_name": "/data/reddylab/Alex/IGVF/data_submissions/processed_data/AIM_2_T_cell_project_1/B2M-High-R2_S8.sorted.bam",
"upload_status": "validated"
},
{
"@id": "/alignment-files/IGVFFI5903FMQU/",
"accession": "IGVFFI5903FMQU",
"aliases": [
"charles-gersbach:cd8-tcells-alignment-crispri-b2m-high-bin-rep3"
],
"assembly": "custom",
"content_type": "alignments",
"creation_timestamp": "2024-10-15T18:53:14.452538+00:00",
"file_format": "bam",
"file_size": 14402145,
"href": "/alignment-files/IGVFFI5903FMQU/@@download/IGVFFI5903FMQU.bam",
"s3_uri": "s3://igvf-files/2024/10/15/a41bbc2f-382e-42f7-a620-32621b576d8a/IGVFFI5903FMQU.bam",
"submitted_file_name": "/data/reddylab/Alex/IGVF/data_submissions/processed_data/AIM_2_T_cell_project_1/B2M-High-R3_S11.sorted.bam",
"upload_status": "validated"
},
{
"@id": "/alignment-files/IGVFFI2031KMAC/",
"accession": "IGVFFI2031KMAC",
"aliases": [
"charles-gersbach:cd8-tcells-alignment-crispri-b2m-low-bin-rep1"
],
"assembly": "custom",
"content_type": "alignments",
"creation_timestamp": "2024-10-15T18:49:53.290947+00:00",
"file_format": "bam",
"file_size": 16408010,
"href": "/alignment-files/IGVFFI2031KMAC/@@download/IGVFFI2031KMAC.bam",
"s3_uri": "s3://igvf-files/2024/10/15/0f423d93-e561-4125-b2c7-d6799cd38298/IGVFFI2031KMAC.bam",
"submitted_file_name": "/data/reddylab/Alex/IGVF/data_submissions/processed_data/AIM_2_T_cell_project_1/B2M-Low-R1_S4.sorted.bam",
"upload_status": "validated"
},
{
"@id": "/alignment-files/IGVFFI3434RUJF/",
"accession": "IGVFFI3434RUJF",
"aliases": [
"charles-gersbach:cd8-tcells-alignment-crispri-b2m-low-bin-rep3"
],
"assembly": "custom",
"content_type": "alignments",
"creation_timestamp": "2024-10-15T18:50:45.352217+00:00",
"file_format": "bam",
"file_size": 12901267,
"href": "/alignment-files/IGVFFI3434RUJF/@@download/IGVFFI3434RUJF.bam",
"s3_uri": "s3://igvf-files/2024/10/15/3a040e6f-d013-4c4a-b5d7-574d7933ba33/IGVFFI3434RUJF.bam",
"submitted_file_name": "/data/reddylab/Alex/IGVF/data_submissions/processed_data/AIM_2_T_cell_project_1/B2M-Low-R3_S10.sorted.bam",
"upload_status": "validated"
},
{
"@id": "/alignment-files/IGVFFI0916WHTV/",
"accession": "IGVFFI0916WHTV",
"aliases": [
"charles-gersbach:cd8-tcells-alignment-crispri-b2m-high-bin-rep1"
],
"assembly": "custom",
"content_type": "alignments",
"creation_timestamp": "2024-10-15T18:52:00.866952+00:00",
"file_format": "bam",
"file_size": 14292602,
"href": "/alignment-files/IGVFFI0916WHTV/@@download/IGVFFI0916WHTV.bam",
"s3_uri": "s3://igvf-files/2024/10/15/f3186e6a-82d7-4bed-a0ae-cf0058e11b2d/IGVFFI0916WHTV.bam",
"submitted_file_name": "/data/reddylab/Alex/IGVF/data_submissions/processed_data/AIM_2_T_cell_project_1/B2M-High-R1_S5.sorted.bam",
"upload_status": "validated"
}
],
"functional_assay_mechanisms": [],
"input_file_sets": [
{
"@id": "/auxiliary-sets/IGVFDS9580JWWG/",
"accession": "IGVFDS9580JWWG",
"aliases": [
"charles-gersbach:cd8-tcells-auxiliary-set-crispri-b2m-low-bin-rep1"
],
"file_set_type": "gRNA sequencing"
},
{
"@id": "/auxiliary-sets/IGVFDS6947GSPF/",
"accession": "IGVFDS6947GSPF",
"aliases": [
"charles-gersbach:cd8-tcells-auxiliary-set-crispri-b2m-low-bin-rep2"
],
"file_set_type": "gRNA sequencing"
},
{
"@id": "/auxiliary-sets/IGVFDS8372HZNT/",
"accession": "IGVFDS8372HZNT",
"aliases": [
"charles-gersbach:cd8-tcells-auxiliary-set-crispri-b2m-low-bin-rep3"
],
"file_set_type": "gRNA sequencing"
},
{
"@id": "/auxiliary-sets/IGVFDS2625BWKZ/",
"accession": "IGVFDS2625BWKZ",
"aliases": [
"charles-gersbach:cd8-tcells-auxiliary-set-crispri-b2m-high-bin-rep1"
],
"file_set_type": "gRNA sequencing"
},
{
"@id": "/auxiliary-sets/IGVFDS3944URNH/",
"accession": "IGVFDS3944URNH",
"aliases": [
"charles-gersbach:cd8-tcells-auxiliary-set-crispri-b2m-high-bin-rep2"
],
"file_set_type": "gRNA sequencing"
},
{
"@id": "/auxiliary-sets/IGVFDS0334XGBU/",
"accession": "IGVFDS0334XGBU",
"aliases": [
"charles-gersbach:cd8-tcells-auxiliary-set-crispri-b2m-high-bin-rep3"
],
"file_set_type": "gRNA sequencing"
}
],
"input_for": [
"/analysis-sets/IGVFDS8839AFQB/"
],
"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": "2024-11-18T21:09:14.185983+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 B2M",
"samples": [
{
"@id": "/primary-cells/IGVFSM1190UUKW/",
"@type": [
"PrimaryCell",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM1190UUKW",
"aliases": [
"charles-gersbach:cd8-tcells-primary-cell-crispri-b2m-low-bin-rep3"
],
"classifications": [
"primary cell"
],
"construct_library_sets": [
"/construct-library-sets/IGVFDS5026WRUO/"
],
"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 b2m) modified with CRISPRi Sa-dCas9, transduced (lentivirus) with a guide library (MOI of 0.4)",
"taxa": "Homo sapiens"
},
{
"@id": "/primary-cells/IGVFSM3427LEEW/",
"@type": [
"PrimaryCell",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM3427LEEW",
"aliases": [
"charles-gersbach:cd8-tcells-primary-cell-crispri-b2m-low-bin-rep2"
],
"classifications": [
"primary cell"
],
"construct_library_sets": [
"/construct-library-sets/IGVFDS5026WRUO/"
],
"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 b2m) modified with CRISPRi Sa-dCas9, transduced (lentivirus) with a guide library (MOI of 0.4)",
"taxa": "Homo sapiens"
},
{
"@id": "/primary-cells/IGVFSM6062UNTJ/",
"@type": [
"PrimaryCell",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM6062UNTJ",
"aliases": [
"charles-gersbach:cd8-tcells-primary-cell-crispri-b2m-high-bin-rep1"
],
"classifications": [
"primary cell"
],
"construct_library_sets": [
"/construct-library-sets/IGVFDS5026WRUO/"
],
"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 b2m) modified with CRISPRi Sa-dCas9, transduced (lentivirus) with a guide library (MOI of 0.4)",
"taxa": "Homo sapiens"
},
{
"@id": "/primary-cells/IGVFSM7452ZWAU/",
"@type": [
"PrimaryCell",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM7452ZWAU",
"aliases": [
"charles-gersbach:cd8-tcells-primary-cell-crispri-b2m-high-bin-rep3"
],
"classifications": [
"primary cell"
],
"construct_library_sets": [
"/construct-library-sets/IGVFDS5026WRUO/"
],
"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 b2m) modified with CRISPRi Sa-dCas9, transduced (lentivirus) with a guide library (MOI of 0.4)",
"taxa": "Homo sapiens"
},
{
"@id": "/primary-cells/IGVFSM4508IIAY/",
"@type": [
"PrimaryCell",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM4508IIAY",
"aliases": [
"charles-gersbach:cd8-tcells-primary-cell-crispri-b2m-high-bin-rep2"
],
"classifications": [
"primary cell"
],
"construct_library_sets": [
"/construct-library-sets/IGVFDS5026WRUO/"
],
"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 b2m) modified with CRISPRi Sa-dCas9, transduced (lentivirus) with a guide library (MOI of 0.4)",
"taxa": "Homo sapiens"
},
{
"@id": "/primary-cells/IGVFSM3073WHFV/",
"@type": [
"PrimaryCell",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM3073WHFV",
"aliases": [
"charles-gersbach:cd8-tcells-primary-cell-crispri-b2m-low-bin-rep1"
],
"classifications": [
"primary cell"
],
"construct_library_sets": [
"/construct-library-sets/IGVFDS5026WRUO/"
],
"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 b2m) 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": "2024-10-15T18:49:53.290947+00:00",
"summary": "CRISPR interference FACS screen targeting B2M: alignments",
"uuid": "1efdbee4-202e-4fce-b0fc-8501614780c2",
"workflows": [
{
"@id": "/workflows/IGVFWF8837BHJV/",
"accession": "IGVFWF8837BHJV",
"name": "Gersbach FACS CRISPR screen workflow"
}
]
}