{
"@context": "/terms/",
"@id": "/alignment-files/IGVFFI2982IKFA/",
"@type": [
"AlignmentFile",
"File",
"Item"
],
"accession": "IGVFFI2982IKFA",
"aliases": [
"charles-gersbach:cd8-tcells-alignment-crispr-ko-tfome-batf3-over-high-bin-rep2"
],
"analysis_step_version": "/analysis-step-versions/f9f6ae88-d515-4e49-9902-deea3cf87703/",
"assay_titles": [
"CRISPR FACS screen"
],
"assembly": "custom",
"audit": {
"INTERNAL_ACTION": [
{
"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/"
}
]
},
"award": {
"@id": "/awards/HG012053/",
"component": "functional characterization"
},
"content_md5sum": "7908274e82883c8a38d34b540915f7cb",
"content_summary": "unfiltered alignments",
"content_type": "alignments",
"controlled_access": false,
"creation_timestamp": "2024-10-15T19:02:33.513982+00:00",
"derived_from": [
"/sequence-files/IGVFFI7895IFCA/"
],
"file_format": "bam",
"file_set": {
"@id": "/analysis-sets/IGVFDS7944XZYE/",
"accession": "IGVFDS7944XZYE",
"file_set_type": "intermediate analysis",
"samples": [
{
"@id": "/primary-cells/IGVFSM3895SURE/",
"accession": "IGVFSM3895SURE",
"classifications": [
"primary cell"
],
"modifications": [
{
"@id": "/crispr-modifications/9fef21f2-9727-4a97-a5a7-c590a637c101/",
"modality": "knockout",
"summary": "CRISPRko Sp-Cas9"
}
],
"sample_terms": [
{
"@id": "/sample-terms/CL_0000909/",
"term_name": "CD8-positive, alpha-beta memory T cell"
}
],
"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/IGVFSM7158ADKU/",
"accession": "IGVFSM7158ADKU",
"classifications": [
"primary cell"
],
"modifications": [
{
"@id": "/crispr-modifications/9fef21f2-9727-4a97-a5a7-c590a637c101/",
"modality": "knockout",
"summary": "CRISPRko Sp-Cas9"
}
],
"sample_terms": [
{
"@id": "/sample-terms/CL_0000909/",
"term_name": "CD8-positive, alpha-beta memory T cell"
}
],
"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/IGVFSM7887TFLH/",
"accession": "IGVFSM7887TFLH",
"classifications": [
"primary cell"
],
"modifications": [
{
"@id": "/crispr-modifications/9fef21f2-9727-4a97-a5a7-c590a637c101/",
"modality": "knockout",
"summary": "CRISPRko Sp-Cas9"
}
],
"sample_terms": [
{
"@id": "/sample-terms/CL_0000909/",
"term_name": "CD8-positive, alpha-beta memory T cell"
}
],
"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/IGVFSM8084QKPW/",
"accession": "IGVFSM8084QKPW",
"classifications": [
"primary cell"
],
"modifications": [
{
"@id": "/crispr-modifications/9fef21f2-9727-4a97-a5a7-c590a637c101/",
"modality": "knockout",
"summary": "CRISPRko Sp-Cas9"
}
],
"sample_terms": [
{
"@id": "/sample-terms/CL_0000909/",
"term_name": "CD8-positive, alpha-beta memory T cell"
}
],
"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"
}
],
"summary": "CRISPR knockout FACS screen targeting IL7R: alignments"
},
"file_size": 473301092,
"filtered": false,
"gene_list_for": [],
"href": "/alignment-files/IGVFFI2982IKFA/@@download/IGVFFI2982IKFA.bam",
"input_file_for": [
"/tabular-files/IGVFFI8017PKLD/"
],
"integrated_in": [],
"lab": {
"@id": "/labs/charles-gersbach/",
"title": "Charles Gersbach, Duke"
},
"loci_list_for": [],
"md5sum": "96315ada5d62a950e8bf1d7cc99d992a",
"read_count": 39592579,
"redacted": false,
"reference_files": [
"/reference-files/IGVFFI0626PVXM/"
],
"release_timestamp": "2024-11-18T21:09:01.746053+00:00",
"s3_uri": "s3://igvf-files/2024/10/15/8909a11a-3349-4d20-89e9-531b08cad315/IGVFFI2982IKFA.bam",
"schema_version": "11",
"status": "released",
"submitted_by": {
"@id": "/users/29f5f78d-ac90-421e-90c6-a90e1dc407a7/",
"title": "Alejandro Barrera"
},
"submitted_file_name": "/data/reddylab/Alex/IGVF/data_submissions/processed_data/AIM_2_T_cell_project_1/pSM74_H3_S12.sorted.bam",
"summary": "custom assembly unfiltered alignments",
"upload_status": "validated",
"uuid": "8909a11a-3349-4d20-89e9-531b08cad315"
}