{
"@context": "/terms/",
"@id": "/analysis-sets/IGVFDS5551EATG/",
"@type": [
"AnalysisSet",
"FileSet",
"Item"
],
"accession": "IGVFDS5551EATG",
"aliases": [
"charles-gersbach:cd8-tcells-intermediate-analysis-crispr-ko-tfome"
],
"assay_titles": [
"CRISPR FACS screen"
],
"audit": {
"INTERNAL_ACTION": [
{
"category": "mismatched status",
"detail": "Released alignment file [IGVFFI6153GXKL](/alignment-files/IGVFFI6153GXKL/) has in progress subobject reference file [IGVFFI0626PVXM](/reference-files/IGVFFI0626PVXM/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/alignment-files/IGVFFI6153GXKL/"
},
{
"category": "mismatched status",
"detail": "Released alignment file [IGVFFI4092OXMN](/alignment-files/IGVFFI4092OXMN/) has in progress subobject reference file [IGVFFI0626PVXM](/reference-files/IGVFFI0626PVXM/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/alignment-files/IGVFFI4092OXMN/"
},
{
"category": "mismatched status",
"detail": "Released alignment file [IGVFFI4927HZXQ](/alignment-files/IGVFFI4927HZXQ/) has in progress subobject reference file [IGVFFI0626PVXM](/reference-files/IGVFFI0626PVXM/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/alignment-files/IGVFFI4927HZXQ/"
},
{
"category": "mismatched status",
"detail": "Released alignment file [IGVFFI9097APHN](/alignment-files/IGVFFI9097APHN/) has in progress subobject reference file [IGVFFI0626PVXM](/reference-files/IGVFFI0626PVXM/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/alignment-files/IGVFFI9097APHN/"
}
],
"WARNING": [
{
"category": "missing age",
"detail": "Primary cell [IGVFSM0466RHGQ](/primary-cells/IGVFSM0466RHGQ/) 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/IGVFSM0466RHGQ/"
},
{
"category": "missing age",
"detail": "Primary cell [IGVFSM2624KTRK](/primary-cells/IGVFSM2624KTRK/) 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/IGVFSM2624KTRK/"
},
{
"category": "missing age",
"detail": "Primary cell [IGVFSM4936HKEW](/primary-cells/IGVFSM4936HKEW/) 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/IGVFSM4936HKEW/"
},
{
"category": "missing age",
"detail": "Primary cell [IGVFSM7226CVDS](/primary-cells/IGVFSM7226CVDS/) 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/IGVFSM7226CVDS/"
}
]
},
"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": "2024-09-20T15:06:22.363118+00:00",
"donors": [
{
"@id": "/human-donors/IGVFDO4646JDEN/",
"accession": "IGVFDO4646JDEN",
"aliases": [
"charles-gersbach:cd8-tcells-donor-23"
],
"sex": "unspecified",
"status": "released",
"taxa": "Homo sapiens"
},
{
"@id": "/human-donors/IGVFDO6692QWLN/",
"accession": "IGVFDO6692QWLN",
"aliases": [
"charles-gersbach:cd8-tcells-donor-24"
],
"sex": "unspecified",
"status": "released",
"taxa": "Homo sapiens"
}
],
"file_set_type": "intermediate analysis",
"files": [
{
"@id": "/alignment-files/IGVFFI6153GXKL/",
"accession": "IGVFFI6153GXKL",
"aliases": [
"charles-gersbach:cd8-tcells-alignment-crispr-ko-tfome-low-bin-rep1"
],
"assembly": "custom",
"content_type": "alignments",
"creation_timestamp": "2024-10-15T18:54:50.923693+00:00",
"file_format": "bam",
"file_size": 549412095,
"href": "/alignment-files/IGVFFI6153GXKL/@@download/IGVFFI6153GXKL.bam",
"s3_uri": "s3://igvf-files/2024/10/15/09c388ad-161b-450a-9248-def1727380ee/IGVFFI6153GXKL.bam",
"submitted_file_name": "/data/reddylab/Alex/IGVF/data_submissions/processed_data/AIM_2_T_cell_project_1/pSM73_L2_S2.sorted.bam",
"upload_status": "validated"
},
{
"@id": "/alignment-files/IGVFFI9097APHN/",
"accession": "IGVFFI9097APHN",
"aliases": [
"charles-gersbach:cd8-tcells-alignment-crispr-ko-tfome-high-bin-rep1"
],
"assembly": "custom",
"content_type": "alignments",
"creation_timestamp": "2024-10-15T19:00:23.460561+00:00",
"file_format": "bam",
"file_size": 589645922,
"href": "/alignment-files/IGVFFI9097APHN/@@download/IGVFFI9097APHN.bam",
"s3_uri": "s3://igvf-files/2024/10/15/e8397125-360f-49a1-83d8-eec87f4ce3cc/IGVFFI9097APHN.bam",
"submitted_file_name": "/data/reddylab/Alex/IGVF/data_submissions/processed_data/AIM_2_T_cell_project_1/pSM73_H2_S5.sorted.bam",
"upload_status": "validated"
},
{
"@id": "/alignment-files/IGVFFI4927HZXQ/",
"accession": "IGVFFI4927HZXQ",
"aliases": [
"charles-gersbach:cd8-tcells-alignment-crispr-ko-tfome-high-bin-rep2"
],
"assembly": "custom",
"content_type": "alignments",
"creation_timestamp": "2024-10-15T19:01:06.392524+00:00",
"file_format": "bam",
"file_size": 552006004,
"href": "/alignment-files/IGVFFI4927HZXQ/@@download/IGVFFI4927HZXQ.bam",
"s3_uri": "s3://igvf-files/2024/10/15/1602bc45-1fb1-4394-a943-f606992bd1b0/IGVFFI4927HZXQ.bam",
"submitted_file_name": "/data/reddylab/Alex/IGVF/data_submissions/processed_data/AIM_2_T_cell_project_1/pSM73_H3_S6.sorted.bam",
"upload_status": "validated"
},
{
"@id": "/alignment-files/IGVFFI4092OXMN/",
"accession": "IGVFFI4092OXMN",
"aliases": [
"charles-gersbach:cd8-tcells-alignment-crispr-ko-tfome-low-bin-rep2"
],
"assembly": "custom",
"content_type": "alignments",
"creation_timestamp": "2024-10-15T18:55:31.970109+00:00",
"file_format": "bam",
"file_size": 476837087,
"href": "/alignment-files/IGVFFI4092OXMN/@@download/IGVFFI4092OXMN.bam",
"s3_uri": "s3://igvf-files/2024/10/15/8bb48d73-3903-4214-9146-8e99ec1c3a6f/IGVFFI4092OXMN.bam",
"submitted_file_name": "/data/reddylab/Alex/IGVF/data_submissions/processed_data/AIM_2_T_cell_project_1/pSM73_L3_S3.sorted.bam",
"upload_status": "validated"
}
],
"functional_assay_mechanisms": [],
"input_file_sets": [
{
"@id": "/auxiliary-sets/IGVFDS1345STXL/",
"accession": "IGVFDS1345STXL",
"aliases": [
"charles-gersbach:cd8-tcells-auxiliary-set-crispr-ko-tfome-low-bin-rep1"
],
"file_set_type": "gRNA sequencing"
},
{
"@id": "/auxiliary-sets/IGVFDS3348HSLB/",
"accession": "IGVFDS3348HSLB",
"aliases": [
"charles-gersbach:cd8-tcells-auxiliary-set-crispr-ko-tfome-low-bin-rep2"
],
"file_set_type": "gRNA sequencing"
},
{
"@id": "/auxiliary-sets/IGVFDS1046ZFUG/",
"accession": "IGVFDS1046ZFUG",
"aliases": [
"charles-gersbach:cd8-tcells-auxiliary-set-crispr-ko-tfome-high-bin-rep1"
],
"file_set_type": "gRNA sequencing"
},
{
"@id": "/auxiliary-sets/IGVFDS4215TFWE/",
"accession": "IGVFDS4215TFWE",
"aliases": [
"charles-gersbach:cd8-tcells-auxiliary-set-crispr-ko-tfome-high-bin-rep2"
],
"file_set_type": "gRNA sequencing"
}
],
"input_for": [
"/analysis-sets/IGVFDS5106XTZH/"
],
"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": "2024-11-18T21:09:11.037356+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/IGVFSM4936HKEW/",
"@type": [
"PrimaryCell",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM4936HKEW",
"aliases": [
"charles-gersbach:cd8-tcells-primary-cell-crispr-ko-tfome-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) modified with CRISPRko Sp-Cas9, transduced (lentivirus) with a guide library (MOI of 0.4)",
"taxa": "Homo sapiens"
},
{
"@id": "/primary-cells/IGVFSM0466RHGQ/",
"@type": [
"PrimaryCell",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM0466RHGQ",
"aliases": [
"charles-gersbach:cd8-tcells-primary-cell-crispr-ko-tfome-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) modified with CRISPRko Sp-Cas9, transduced (lentivirus) with a guide library (MOI of 0.4)",
"taxa": "Homo sapiens"
},
{
"@id": "/primary-cells/IGVFSM7226CVDS/",
"@type": [
"PrimaryCell",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM7226CVDS",
"aliases": [
"charles-gersbach:cd8-tcells-primary-cell-crispr-ko-tfome-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) modified with CRISPRko Sp-Cas9, transduced (lentivirus) with a guide library (MOI of 0.4)",
"taxa": "Homo sapiens"
},
{
"@id": "/primary-cells/IGVFSM2624KTRK/",
"@type": [
"PrimaryCell",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM2624KTRK",
"aliases": [
"charles-gersbach:cd8-tcells-primary-cell-crispr-ko-tfome-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) 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": "2024-10-15T18:54:50.923693+00:00",
"summary": "CRISPR knockout FACS screen targeting IL7R: alignments",
"uuid": "54701b6c-b2e1-48f6-bb2f-460299b7a7c8",
"workflows": [
{
"@id": "/workflows/IGVFWF8837BHJV/",
"accession": "IGVFWF8837BHJV",
"name": "Gersbach FACS CRISPR screen workflow"
}
]
}