{
"@context": "/terms/",
"@id": "/alignment-files/IGVFFI4242DKSL/",
"@type": [
"AlignmentFile",
"File",
"Item"
],
"accession": "IGVFFI4242DKSL",
"aliases": [
"charles-gersbach:cd8-tcells-alignment-crispri-b2m-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 [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/"
}
]
},
"award": {
"@id": "/awards/HG012053/",
"component": "functional characterization"
},
"content_md5sum": "875aaaeb628786c0520de8d9ad0a6047",
"content_summary": "unfiltered alignments",
"content_type": "alignments",
"controlled_access": false,
"creation_timestamp": "2024-10-15T18:52:40.653370+00:00",
"derived_from": [
"/sequence-files/IGVFFI0790UGVP/"
],
"file_format": "bam",
"file_set": {
"@id": "/analysis-sets/IGVFDS2716FVEL/",
"accession": "IGVFDS2716FVEL",
"file_set_type": "intermediate analysis",
"samples": [
{
"@id": "/primary-cells/IGVFSM1190UUKW/",
"accession": "IGVFSM1190UUKW",
"classifications": [
"primary cell"
],
"modifications": [
{
"@id": "/crispr-modifications/95393c9a-637d-43f6-baf9-662e45d28d61/",
"modality": "interference",
"summary": "CRISPRi Sa-dCas9"
}
],
"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 b2m) modified with CRISPRi Sa-dCas9, transduced (lentivirus) with a guide library (MOI of 0.4)",
"taxa": "Homo sapiens"
},
{
"@id": "/primary-cells/IGVFSM3427LEEW/",
"accession": "IGVFSM3427LEEW",
"classifications": [
"primary cell"
],
"modifications": [
{
"@id": "/crispr-modifications/95393c9a-637d-43f6-baf9-662e45d28d61/",
"modality": "interference",
"summary": "CRISPRi Sa-dCas9"
}
],
"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 b2m) modified with CRISPRi Sa-dCas9, transduced (lentivirus) with a guide library (MOI of 0.4)",
"taxa": "Homo sapiens"
},
{
"@id": "/primary-cells/IGVFSM6062UNTJ/",
"accession": "IGVFSM6062UNTJ",
"classifications": [
"primary cell"
],
"modifications": [
{
"@id": "/crispr-modifications/95393c9a-637d-43f6-baf9-662e45d28d61/",
"modality": "interference",
"summary": "CRISPRi Sa-dCas9"
}
],
"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 b2m) modified with CRISPRi Sa-dCas9, transduced (lentivirus) with a guide library (MOI of 0.4)",
"taxa": "Homo sapiens"
},
{
"@id": "/primary-cells/IGVFSM7452ZWAU/",
"accession": "IGVFSM7452ZWAU",
"classifications": [
"primary cell"
],
"modifications": [
{
"@id": "/crispr-modifications/95393c9a-637d-43f6-baf9-662e45d28d61/",
"modality": "interference",
"summary": "CRISPRi Sa-dCas9"
}
],
"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 b2m) modified with CRISPRi Sa-dCas9, transduced (lentivirus) with a guide library (MOI of 0.4)",
"taxa": "Homo sapiens"
},
{
"@id": "/primary-cells/IGVFSM4508IIAY/",
"accession": "IGVFSM4508IIAY",
"classifications": [
"primary cell"
],
"modifications": [
{
"@id": "/crispr-modifications/95393c9a-637d-43f6-baf9-662e45d28d61/",
"modality": "interference",
"summary": "CRISPRi Sa-dCas9"
}
],
"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 b2m) modified with CRISPRi Sa-dCas9, transduced (lentivirus) with a guide library (MOI of 0.4)",
"taxa": "Homo sapiens"
},
{
"@id": "/primary-cells/IGVFSM3073WHFV/",
"accession": "IGVFSM3073WHFV",
"classifications": [
"primary cell"
],
"modifications": [
{
"@id": "/crispr-modifications/95393c9a-637d-43f6-baf9-662e45d28d61/",
"modality": "interference",
"summary": "CRISPRi Sa-dCas9"
}
],
"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 b2m) modified with CRISPRi Sa-dCas9, transduced (lentivirus) with a guide library (MOI of 0.4)",
"taxa": "Homo sapiens"
}
],
"summary": "CRISPR interference FACS screen targeting B2M: alignments"
},
"file_size": 16445235,
"filtered": false,
"gene_list_for": [],
"href": "/alignment-files/IGVFFI4242DKSL/@@download/IGVFFI4242DKSL.bam",
"input_file_for": [
"/tabular-files/IGVFFI0520IBDF/"
],
"integrated_in": [],
"lab": {
"@id": "/labs/charles-gersbach/",
"title": "Charles Gersbach, Duke"
},
"loci_list_for": [],
"md5sum": "7c92f5e5939f7164ee6a6d635a5c7a7d",
"read_count": 976457,
"redacted": false,
"reference_files": [
"/reference-files/IGVFFI9036JJXB/"
],
"release_timestamp": "2024-11-18T21:09:14.381944+00:00",
"s3_uri": "s3://igvf-files/2024/10/15/b5ef1cc3-392b-4056-af6b-b5ba5853cacd/IGVFFI4242DKSL.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/B2M-High-R2_S8.sorted.bam",
"summary": "custom assembly unfiltered alignments",
"upload_status": "validated",
"uuid": "b5ef1cc3-392b-4056-af6b-b5ba5853cacd"
}