{
"@context": "/terms/",
"@id": "/analysis-sets/IGVFDS7944XZYE/",
"@type": [
"AnalysisSet",
"FileSet",
"Item"
],
"accession": "IGVFDS7944XZYE",
"aliases": [
"charles-gersbach:cd8-tcells-intermediate-analysis-crispr-ko-tfome-batf3-over"
],
"assay_titles": [
"CRISPR FACS screen"
],
"audit": {
"INTERNAL_ACTION": [
{
"category": "mismatched status",
"detail": "Released alignment file [IGVFFI1995JCIO](/alignment-files/IGVFFI1995JCIO/) has in progress subobject reference file [IGVFFI0626PVXM](/reference-files/IGVFFI0626PVXM/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/alignment-files/IGVFFI1995JCIO/"
},
{
"category": "mismatched status",
"detail": "Released alignment file [IGVFFI8725GDOS](/alignment-files/IGVFFI8725GDOS/) has in progress subobject reference file [IGVFFI0626PVXM](/reference-files/IGVFFI0626PVXM/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/alignment-files/IGVFFI8725GDOS/"
},
{
"category": "mismatched status",
"detail": "Released alignment file [IGVFFI5819OXDI](/alignment-files/IGVFFI5819OXDI/) has in progress subobject reference file [IGVFFI0626PVXM](/reference-files/IGVFFI0626PVXM/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/alignment-files/IGVFFI5819OXDI/"
},
{
"category": "mismatched status",
"detail": "Released alignment file [IGVFFI2982IKFA](/alignment-files/IGVFFI2982IKFA/) has in progress subobject reference file [IGVFFI0626PVXM](/reference-files/IGVFFI0626PVXM/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/alignment-files/IGVFFI2982IKFA/"
}
],
"WARNING": [
{
"category": "missing age",
"detail": "Primary cell [IGVFSM3895SURE](/primary-cells/IGVFSM3895SURE/) 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/IGVFSM3895SURE/"
},
{
"category": "missing age",
"detail": "Primary cell [IGVFSM7158ADKU](/primary-cells/IGVFSM7158ADKU/) 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/IGVFSM7158ADKU/"
},
{
"category": "missing age",
"detail": "Primary cell [IGVFSM8084QKPW](/primary-cells/IGVFSM8084QKPW/) 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/IGVFSM8084QKPW/"
},
{
"category": "missing age",
"detail": "Primary cell [IGVFSM7887TFLH](/primary-cells/IGVFSM7887TFLH/) 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/IGVFSM7887TFLH/"
}
]
},
"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": "2024-09-20T15:06:24.624343+00:00",
"donors": [
{
"@id": "/human-donors/IGVFDO2763RVOY/",
"accession": "IGVFDO2763RVOY",
"aliases": [
"charles-gersbach:cd8-tcells-donor-26"
],
"sex": "unspecified",
"status": "released",
"taxa": "Homo sapiens"
},
{
"@id": "/human-donors/IGVFDO8306NDTY/",
"accession": "IGVFDO8306NDTY",
"aliases": [
"charles-gersbach:cd8-tcells-donor-25"
],
"sex": "unspecified",
"status": "released",
"taxa": "Homo sapiens"
}
],
"file_set_type": "intermediate analysis",
"files": [
{
"@id": "/alignment-files/IGVFFI2982IKFA/",
"accession": "IGVFFI2982IKFA",
"aliases": [
"charles-gersbach:cd8-tcells-alignment-crispr-ko-tfome-batf3-over-high-bin-rep2"
],
"assembly": "custom",
"content_type": "alignments",
"creation_timestamp": "2024-10-15T19:02:33.513982+00:00",
"file_format": "bam",
"file_size": 473301092,
"href": "/alignment-files/IGVFFI2982IKFA/@@download/IGVFFI2982IKFA.bam",
"s3_uri": "s3://igvf-files/2024/10/15/8909a11a-3349-4d20-89e9-531b08cad315/IGVFFI2982IKFA.bam",
"submitted_file_name": "/data/reddylab/Alex/IGVF/data_submissions/processed_data/AIM_2_T_cell_project_1/pSM74_H3_S12.sorted.bam",
"upload_status": "validated"
},
{
"@id": "/alignment-files/IGVFFI1995JCIO/",
"accession": "IGVFFI1995JCIO",
"aliases": [
"charles-gersbach:cd8-tcells-alignment-crispr-ko-tfome-batf3-over-low-bin-rep2"
],
"assembly": "custom",
"content_type": "alignments",
"creation_timestamp": "2024-10-15T18:56:56.853098+00:00",
"file_format": "bam",
"file_size": 446304076,
"href": "/alignment-files/IGVFFI1995JCIO/@@download/IGVFFI1995JCIO.bam",
"s3_uri": "s3://igvf-files/2024/10/15/707adf34-3cf8-4e02-a73d-984ebe2fea50/IGVFFI1995JCIO.bam",
"submitted_file_name": "/data/reddylab/Alex/IGVF/data_submissions/processed_data/AIM_2_T_cell_project_1/pSM74_L3_S9.sorted.bam",
"upload_status": "validated"
},
{
"@id": "/alignment-files/IGVFFI8725GDOS/",
"accession": "IGVFFI8725GDOS",
"aliases": [
"charles-gersbach:cd8-tcells-alignment-crispr-ko-tfome-batf3-over-low-bin-rep1"
],
"assembly": "custom",
"content_type": "alignments",
"creation_timestamp": "2024-10-15T18:56:14.664713+00:00",
"file_format": "bam",
"file_size": 379707686,
"href": "/alignment-files/IGVFFI8725GDOS/@@download/IGVFFI8725GDOS.bam",
"s3_uri": "s3://igvf-files/2024/10/15/a85afe00-bbc5-43bd-b4d2-b93065b4134b/IGVFFI8725GDOS.bam",
"submitted_file_name": "/data/reddylab/Alex/IGVF/data_submissions/processed_data/AIM_2_T_cell_project_1/pSM74_L2_S8.sorted.bam",
"upload_status": "validated"
},
{
"@id": "/alignment-files/IGVFFI5819OXDI/",
"accession": "IGVFFI5819OXDI",
"aliases": [
"charles-gersbach:cd8-tcells-alignment-crispr-ko-tfome-batf3-over-high-bin-rep1"
],
"assembly": "custom",
"content_type": "alignments",
"creation_timestamp": "2024-10-15T19:01:50.213063+00:00",
"file_format": "bam",
"file_size": 437309053,
"href": "/alignment-files/IGVFFI5819OXDI/@@download/IGVFFI5819OXDI.bam",
"s3_uri": "s3://igvf-files/2024/10/15/d532528a-5117-45d5-b838-672f556de1ff/IGVFFI5819OXDI.bam",
"submitted_file_name": "/data/reddylab/Alex/IGVF/data_submissions/processed_data/AIM_2_T_cell_project_1/pSM74_H2_S11.sorted.bam",
"upload_status": "validated"
}
],
"functional_assay_mechanisms": [],
"input_file_sets": [
{
"@id": "/auxiliary-sets/IGVFDS2606RJRX/",
"accession": "IGVFDS2606RJRX",
"aliases": [
"charles-gersbach:cd8-tcells-auxiliary-set-crispr-ko-tfome-batf3-over-low-bin-rep1"
],
"file_set_type": "gRNA sequencing"
},
{
"@id": "/auxiliary-sets/IGVFDS4170XDRQ/",
"accession": "IGVFDS4170XDRQ",
"aliases": [
"charles-gersbach:cd8-tcells-auxiliary-set-crispr-ko-tfome-batf3-over-low-bin-rep2"
],
"file_set_type": "gRNA sequencing"
},
{
"@id": "/auxiliary-sets/IGVFDS3370BGRA/",
"accession": "IGVFDS3370BGRA",
"aliases": [
"charles-gersbach:cd8-tcells-auxiliary-set-crispr-ko-tfome-batf3-over-high-bin-rep1"
],
"file_set_type": "gRNA sequencing"
},
{
"@id": "/auxiliary-sets/IGVFDS2210LUUT/",
"accession": "IGVFDS2210LUUT",
"aliases": [
"charles-gersbach:cd8-tcells-auxiliary-set-crispr-ko-tfome-batf3-over-high-bin-rep2"
],
"file_set_type": "gRNA sequencing"
}
],
"input_for": [
"/analysis-sets/IGVFDS8364HJHL/"
],
"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": "2024-11-18T21:09:01.215467+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 IL7R",
"samples": [
{
"@id": "/primary-cells/IGVFSM7887TFLH/",
"@type": [
"PrimaryCell",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM7887TFLH",
"aliases": [
"charles-gersbach:cd8-tcells-primary-cell-crispr-ko-tfome-batf3-over-high-bin-rep2"
],
"classifications": [
"primary cell"
],
"construct_library_sets": [
"/construct-library-sets/IGVFDS3667PLQB/"
],
"modifications": [
{
"@id": "/crispr-modifications/9fef21f2-9727-4a97-a5a7-c590a637c101/",
"modality": "knockout"
}
],
"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 IL7R in cells overexpressing BATF3) modified with CRISPRko Sp-Cas9, transduced (lentivirus) with a guide library (MOI of 0.4)",
"taxa": "Homo sapiens"
},
{
"@id": "/primary-cells/IGVFSM7158ADKU/",
"@type": [
"PrimaryCell",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM7158ADKU",
"aliases": [
"charles-gersbach:cd8-tcells-primary-cell-crispr-ko-tfome-batf3-over-low-bin-rep2"
],
"classifications": [
"primary cell"
],
"construct_library_sets": [
"/construct-library-sets/IGVFDS3667PLQB/"
],
"modifications": [
{
"@id": "/crispr-modifications/9fef21f2-9727-4a97-a5a7-c590a637c101/",
"modality": "knockout"
}
],
"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 IL7R in cells overexpressing BATF3) modified with CRISPRko Sp-Cas9, transduced (lentivirus) with a guide library (MOI of 0.4)",
"taxa": "Homo sapiens"
},
{
"@id": "/primary-cells/IGVFSM8084QKPW/",
"@type": [
"PrimaryCell",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM8084QKPW",
"aliases": [
"charles-gersbach:cd8-tcells-primary-cell-crispr-ko-tfome-batf3-over-high-bin-rep1"
],
"classifications": [
"primary cell"
],
"construct_library_sets": [
"/construct-library-sets/IGVFDS3667PLQB/"
],
"modifications": [
{
"@id": "/crispr-modifications/9fef21f2-9727-4a97-a5a7-c590a637c101/",
"modality": "knockout"
}
],
"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 IL7R in cells overexpressing BATF3) modified with CRISPRko Sp-Cas9, transduced (lentivirus) with a guide library (MOI of 0.4)",
"taxa": "Homo sapiens"
},
{
"@id": "/primary-cells/IGVFSM3895SURE/",
"@type": [
"PrimaryCell",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM3895SURE",
"aliases": [
"charles-gersbach:cd8-tcells-primary-cell-crispr-ko-tfome-batf3-over-low-bin-rep1"
],
"classifications": [
"primary cell"
],
"construct_library_sets": [
"/construct-library-sets/IGVFDS3667PLQB/"
],
"modifications": [
{
"@id": "/crispr-modifications/9fef21f2-9727-4a97-a5a7-c590a637c101/",
"modality": "knockout"
}
],
"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 IL7R in cells overexpressing BATF3) modified with CRISPRko Sp-Cas9, 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": "2024-10-15T18:56:14.664713+00:00",
"summary": "CRISPR knockout FACS screen targeting IL7R: alignments",
"uuid": "c9181de6-0db8-4056-a95d-030bb2a5b02d",
"workflows": [
{
"@id": "/workflows/IGVFWF8837BHJV/",
"accession": "IGVFWF8837BHJV",
"name": "Gersbach FACS CRISPR screen workflow"
}
]
}