{
"@context": "/terms/",
"@id": "/matrix-files/IGVFFI0296HFSP/",
"@type": [
"MatrixFile",
"File",
"Item"
],
"accession": "IGVFFI0296HFSP",
"aliases": [
"charles-gersbach:cd8-tcells-perturb-seq-10x-5prime-mm-crispri-rep1"
],
"analysis_step_version": "/analysis-step-versions/fbd5e8fb-4206-4b43-92d6-922cdfe1338b/",
"assay_titles": [
"Perturb-seq"
],
"audit": {
"NOT_COMPLIANT": [
{
"category": "missing file format specifications",
"detail": "Matrix file [IGVFFI0296HFSP](/matrix-files/IGVFFI0296HFSP/) has no `file_format_specifications`. Matrix files are expected to link to a file format specifications document describing the axes and layers of the file.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_file_no_file_format_specifications",
"path": "/matrix-files/IGVFFI0296HFSP/"
}
]
},
"award": {
"@id": "/awards/HG012053/",
"component": "functional characterization"
},
"content_md5sum": "56f1371041624147e07cb088e1c920da",
"content_summary": "gene by gene expression by CRISPR guide capture in filtered feature barcode matrix",
"content_type": "filtered feature barcode matrix",
"creation_timestamp": "2024-09-22T17:45:10.874265+00:00",
"derived_from": [
"/sequence-files/IGVFFI2739KXTR/",
"/sequence-files/IGVFFI1822KONB/",
"/sequence-files/IGVFFI7019QDVE/",
"/sequence-files/IGVFFI7645VURG/",
"/sequence-files/IGVFFI1399GORD/",
"/sequence-files/IGVFFI7384WZTF/",
"/sequence-files/IGVFFI6523JOQO/",
"/sequence-files/IGVFFI7716LYLL/",
"/sequence-files/IGVFFI5465GDKG/",
"/sequence-files/IGVFFI1875HEKG/",
"/sequence-files/IGVFFI3480BTJU/",
"/sequence-files/IGVFFI5492CFOS/",
"/sequence-files/IGVFFI4222KPGA/",
"/sequence-files/IGVFFI7250XPAW/",
"/sequence-files/IGVFFI9522NHQX/",
"/sequence-files/IGVFFI5512GZXV/"
],
"file_format": "tar",
"file_set": {
"@id": "/analysis-sets/IGVFDS9445RJOU/",
"@type": [
"AnalysisSet",
"FileSet",
"Item"
],
"accession": "IGVFDS9445RJOU",
"file_set_type": "principal analysis",
"samples": [
{
"@id": "/primary-cells/IGVFSM3795JDHP/",
"@type": [
"PrimaryCell",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM3795JDHP",
"classifications": [
"primary cell"
],
"modifications": [
{
"@id": "/crispr-modifications/95393c9a-637d-43f6-baf9-662e45d28d61/",
"modality": "interference",
"status": "released",
"summary": "CRISPRi Sa-dCas9-KOX1-KRAB"
}
],
"sample_terms": [
{
"@id": "/sample-terms/CL_0000909/",
"status": "released",
"term_name": "CD8-positive, alpha-beta memory T cell"
}
],
"status": "released",
"summary": "Homo sapiens CD8-positive, alpha-beta memory T cell modified with CRISPRi Sa-dCas9-KOX1-KRAB, transduced (lentivirus) with a guide library (MOI of 0.4)",
"taxa": "Homo sapiens"
},
{
"@id": "/primary-cells/IGVFSM5189UBOI/",
"@type": [
"PrimaryCell",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM5189UBOI",
"classifications": [
"primary cell"
],
"modifications": [
{
"@id": "/crispr-modifications/95393c9a-637d-43f6-baf9-662e45d28d61/",
"modality": "interference",
"status": "released",
"summary": "CRISPRi Sa-dCas9-KOX1-KRAB"
}
],
"sample_terms": [
{
"@id": "/sample-terms/CL_0000909/",
"status": "released",
"term_name": "CD8-positive, alpha-beta memory T cell"
}
],
"status": "released",
"summary": "Homo sapiens CD8-positive, alpha-beta memory T cell modified with CRISPRi Sa-dCas9-KOX1-KRAB, transduced (lentivirus) with a guide library (MOI of 0.4)",
"taxa": "Homo sapiens"
},
{
"@id": "/primary-cells/IGVFSM2747RJFY/",
"@type": [
"PrimaryCell",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM2747RJFY",
"classifications": [
"primary cell"
],
"modifications": [
{
"@id": "/crispr-modifications/95393c9a-637d-43f6-baf9-662e45d28d61/",
"modality": "interference",
"status": "released",
"summary": "CRISPRi Sa-dCas9-KOX1-KRAB"
}
],
"sample_terms": [
{
"@id": "/sample-terms/CL_0000909/",
"status": "released",
"term_name": "CD8-positive, alpha-beta memory T cell"
}
],
"status": "released",
"summary": "Homo sapiens CD8-positive, alpha-beta memory T cell modified with CRISPRi Sa-dCas9-KOX1-KRAB, transduced (lentivirus) with a guide library (MOI of 0.4)",
"taxa": "Homo sapiens"
}
],
"status": "released",
"summary": "interference Perturb-seq: differential gene expression quantifications, filtered feature barcode matrix"
},
"file_size": 382505366,
"gene_list_for": [],
"href": "/matrix-files/IGVFFI0296HFSP/@@download/IGVFFI0296HFSP.tar.gz",
"input_file_for": [
"/tabular-files/IGVFFI5198JCCU/",
"/tabular-files/IGVFFI9686JEQV/"
],
"integrated_in": [],
"lab": {
"@id": "/labs/charles-gersbach/",
"title": "Charles Gersbach, Duke"
},
"loci_list_for": [],
"md5sum": "016c46d0c12fab6e465c32a04c1c577b",
"principal_dimension": "gene",
"quality_metrics": [],
"reference_files": [
"/reference-files/IGVFFI8553BTYV/"
],
"release_timestamp": "2024-10-18T19:50:08.516814+00:00",
"s3_uri": "s3://igvf-files/2024/09/22/b9df5b53-ddfc-4aba-aa69-5f572c717d2a/IGVFFI0296HFSP.tar.gz",
"schema_version": "7",
"secondary_dimensions": [
"gene expression",
"CRISPR guide capture"
],
"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/CRISPRi_D1_10x.tar.gz",
"summary": "gene by gene expression by CRISPR guide capture in filtered feature barcode matrix",
"upload_status": "validated",
"uuid": "b9df5b53-ddfc-4aba-aa69-5f572c717d2a",
"workflow": {
"@id": "/workflows/IGVFWF7562QXLM/",
"name": "Cell Ranger Gene Count Pipeline"
}
}