{
"@context": "/terms/",
"@id": "/tabular-files/IGVFFI4410YZQZ/",
"@type": [
"TabularFile",
"File",
"Item"
],
"accession": "IGVFFI4410YZQZ",
"aliases": [
"gary-hon:WTC11_CM_Pilot2_Mini_PB9_PrimaryAnalysis_DE_local"
],
"analysis_step_version": "/analysis-step-versions/4cfc022a-ff63-4d13-99f7-257a6bfe4bd7/",
"assay_titles": [
"Perturb-seq"
],
"assembly": "GRCh38",
"audit": {},
"award": {
"@id": "/awards/HG011996/",
"component": "functional characterization"
},
"barcode_map_for": [],
"checkfiles_version": "v16",
"content_md5sum": "bb47f7aa7953e65e1f9d937c395052c4",
"content_type": "unfiltered local differential expression",
"controlled_access": false,
"creation_timestamp": "2024-12-18T20:48:34.756501+00:00",
"derived_from": [
"/matrix-files/IGVFFI8767IWEB/",
"/matrix-files/IGVFFI8929UOQW/"
],
"file_format": "csv",
"file_format_specifications": [
"/documents/88d2ed1f-3c0a-4df4-b14f-c203d028899f/"
],
"file_set": {
"@id": "/analysis-sets/IGVFDS4252LFRU/",
"@type": [
"AnalysisSet",
"FileSet",
"Item"
],
"accession": "IGVFDS4252LFRU",
"data_use_limitation_summaries": [
"no certificate"
],
"file_set_type": "principal analysis",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM8072YOLO/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM8072YOLO",
"classifications": [
"differentiated cell specimen"
],
"modifications": [
{
"@id": "/crispr-modifications/0a63b754-eca4-44aa-bbc2-fccdc6c44fb5/",
"modality": "interference",
"status": "preview",
"summary": "CRISPRi Sp-dCas9"
}
],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0009747/",
"status": "released",
"term_name": "GM25256 (WTC-11)"
}
],
"status": "preview",
"summary": "Homo sapiens (male) GM25256 (WTC-11) differentiated cell specimen induced to cardiac muscle cell for 12 days (cellular sub pool: subpool_LW437) modified with CRISPRi Sp-dCas9, 3 week(s) after transfection with a guide library",
"targeted_sample_term": {
"@id": "/sample-terms/CL_0000746/",
"status": "released",
"term_name": "cardiac muscle cell"
},
"taxa": "Homo sapiens"
},
{
"@id": "/in-vitro-systems/IGVFSM4418NJET/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM4418NJET",
"classifications": [
"differentiated cell specimen"
],
"modifications": [
{
"@id": "/crispr-modifications/0a63b754-eca4-44aa-bbc2-fccdc6c44fb5/",
"modality": "interference",
"status": "preview",
"summary": "CRISPRi Sp-dCas9"
}
],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0009747/",
"status": "released",
"term_name": "GM25256 (WTC-11)"
}
],
"status": "preview",
"summary": "Homo sapiens (male) GM25256 (WTC-11) differentiated cell specimen induced to cardiac muscle cell for 12 days (cellular sub pool: subpool_LW435) modified with CRISPRi Sp-dCas9, 3 week(s) after transfection with a guide library",
"targeted_sample_term": {
"@id": "/sample-terms/CL_0000746/",
"status": "released",
"term_name": "cardiac muscle cell"
},
"taxa": "Homo sapiens"
},
{
"@id": "/in-vitro-systems/IGVFSM8889XSOR/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM8889XSOR",
"classifications": [
"differentiated cell specimen"
],
"modifications": [
{
"@id": "/crispr-modifications/0a63b754-eca4-44aa-bbc2-fccdc6c44fb5/",
"modality": "interference",
"status": "preview",
"summary": "CRISPRi Sp-dCas9"
}
],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0009747/",
"status": "released",
"term_name": "GM25256 (WTC-11)"
}
],
"status": "preview",
"summary": "Homo sapiens (male) GM25256 (WTC-11) differentiated cell specimen induced to cardiac muscle cell for 12 days (cellular sub pool: subpool_LW436) modified with CRISPRi Sp-dCas9, 3 week(s) after transfection with a guide library",
"targeted_sample_term": {
"@id": "/sample-terms/CL_0000746/",
"status": "released",
"term_name": "cardiac muscle cell"
},
"taxa": "Homo sapiens"
},
{
"@id": "/in-vitro-systems/IGVFSM2176YXFG/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM2176YXFG",
"classifications": [
"differentiated cell specimen"
],
"modifications": [
{
"@id": "/crispr-modifications/0a63b754-eca4-44aa-bbc2-fccdc6c44fb5/",
"modality": "interference",
"status": "preview",
"summary": "CRISPRi Sp-dCas9"
}
],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0009747/",
"status": "released",
"term_name": "GM25256 (WTC-11)"
}
],
"status": "preview",
"summary": "Homo sapiens (male) GM25256 (WTC-11) differentiated cell specimen induced to cardiac muscle cell for 12 days (cellular sub pool: subpool_LW438) modified with CRISPRi Sp-dCas9, 3 week(s) after transfection with a guide library",
"targeted_sample_term": {
"@id": "/sample-terms/CL_0000746/",
"status": "released",
"term_name": "cardiac muscle cell"
},
"taxa": "Homo sapiens"
}
],
"status": "preview",
"summary": "CRISPR interference Perturb-seq integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci: filtered feature barcode matrix, raw feature barcode matrix, sparse gene count matrix, unfiltered global differential expression, unfiltered local differential expression"
},
"file_size": 6592,
"gene_list_for": [],
"href": "/tabular-files/IGVFFI4410YZQZ/@@download/IGVFFI4410YZQZ.csv.gz",
"input_file_for": [],
"integrated_in": [],
"lab": {
"@id": "/labs/gary-hon/",
"title": "Gary Hon, UT"
},
"loci_list_for": [],
"md5sum": "5529ced80d67d34b604a49a2e7a0404a",
"primer_design_for": [],
"quality_metrics": [],
"s3_uri": "s3://igvf-files/2024/12/18/94cb8573-25f3-4a4d-bcc7-7b55f3002a56/IGVFFI4410YZQZ.csv.gz",
"schema_version": "15",
"status": "preview",
"submitted_by": {
"@id": "/users/b05645f1-2d56-4a5e-b272-4601e555a3fa/",
"title": "Mpathi Nzima"
},
"submitted_file_name": "/project/GCRB/Hon_lab/s215194/IGVF/data_submission/reference_files/WTC11_CM_Pilot2_Mini_PB9_PrimaryAnalysis_DE_local.csv.gz",
"summary": "GRCh38 GENCODE 32 unfiltered local differential expression",
"transcriptome_annotation": "GENCODE 32",
"upload_status": "validated",
"uuid": "94cb8573-25f3-4a4d-bcc7-7b55f3002a56",
"workflow": {
"@id": "/workflows/IGVFWF0190YALU/",
"name": "Hon Perturb-seq Workflow",
"uniform_pipeline": false
}
}