{
"@context": "/terms/",
"@id": "/matrix-files/IGVFFI8767IWEB/",
"@type": [
"MatrixFile",
"File",
"Item"
],
"accession": "IGVFFI8767IWEB",
"aliases": [
"gary-hon:WTC11_CM_Pilot2_Mini_PB9_PrimaryAnalysis_h5"
],
"analysis_step_version": "/analysis-step-versions/65c095ee-8330-48d0-bc03-d930326fe393/",
"assay_titles": [
"Perturb-seq"
],
"audit": {
"INTERNAL_ACTION": [
{
"category": "mismatched status",
"detail": "Preview matrix file [IGVFFI8767IWEB](/matrix-files/IGVFFI8767IWEB/) has in progress subobject analysis step version [65c095ee-8330-48d0-bc03-d930326fe393](/analysis-step-versions/65c095ee-8330-48d0-bc03-d930326fe393/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/matrix-files/IGVFFI8767IWEB/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing file format specifications",
"detail": "Matrix file [IGVFFI8767IWEB](/matrix-files/IGVFFI8767IWEB/) 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/IGVFFI8767IWEB/"
}
]
},
"award": {
"@id": "/awards/HG011996/",
"component": "functional characterization"
},
"content_summary": "cell by UMI count in filtered feature barcode matrix",
"content_type": "filtered feature barcode matrix",
"creation_timestamp": "2024-12-17T23:44:11.744242+00:00",
"derived_from": [
"/sequence-files/IGVFFI1994YPNP/",
"/sequence-files/IGVFFI0266LNZW/",
"/sequence-files/IGVFFI9977BZMF/",
"/sequence-files/IGVFFI7972XHRF/",
"/sequence-files/IGVFFI8257WJQZ/",
"/sequence-files/IGVFFI7650HNVF/",
"/sequence-files/IGVFFI5492QZLT/",
"/sequence-files/IGVFFI5457CMID/",
"/sequence-files/IGVFFI8547HGDV/",
"/sequence-files/IGVFFI0312LDQL/",
"/sequence-files/IGVFFI9725RURB/",
"/sequence-files/IGVFFI9965CSOU/",
"/sequence-files/IGVFFI7391DKIW/",
"/sequence-files/IGVFFI0616HDUP/",
"/sequence-files/IGVFFI8911SHCH/",
"/sequence-files/IGVFFI5764VRNL/",
"/sequence-files/IGVFFI1163JWIL/",
"/sequence-files/IGVFFI5776RSQZ/",
"/sequence-files/IGVFFI2584JXRS/",
"/sequence-files/IGVFFI0178AEKX/",
"/sequence-files/IGVFFI1889WATW/",
"/sequence-files/IGVFFI0936YGAN/",
"/sequence-files/IGVFFI9720JHJW/",
"/sequence-files/IGVFFI3170CQKI/",
"/sequence-files/IGVFFI6775MOMC/",
"/sequence-files/IGVFFI5747FEKP/",
"/sequence-files/IGVFFI7723HURE/",
"/sequence-files/IGVFFI2630YDCC/",
"/sequence-files/IGVFFI9007JSBK/",
"/sequence-files/IGVFFI6210OCQP/",
"/sequence-files/IGVFFI9606HEAN/",
"/sequence-files/IGVFFI9049KFCN/",
"/sequence-files/IGVFFI1394EWKL/",
"/sequence-files/IGVFFI7023BMQV/",
"/sequence-files/IGVFFI8600ACAI/",
"/sequence-files/IGVFFI1686TDZN/",
"/sequence-files/IGVFFI3598BJXU/",
"/sequence-files/IGVFFI9922VQUJ/",
"/sequence-files/IGVFFI2499SPMY/",
"/sequence-files/IGVFFI9761CWFK/",
"/sequence-files/IGVFFI2410SQSR/",
"/sequence-files/IGVFFI9959PZPC/",
"/sequence-files/IGVFFI9583JOVR/",
"/sequence-files/IGVFFI0287KKJM/",
"/sequence-files/IGVFFI7807KQXP/",
"/sequence-files/IGVFFI1618BPQM/",
"/sequence-files/IGVFFI3053AQRM/",
"/sequence-files/IGVFFI7701ZMBO/"
],
"file_format": "hdf5",
"file_set": {
"@id": "/analysis-sets/IGVFDS4252LFRU/",
"@type": [
"AnalysisSet",
"FileSet",
"Item"
],
"accession": "IGVFDS4252LFRU",
"file_set_type": "principal analysis",
"samples": [
{
"@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"
},
{
"@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/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"
}
],
"status": "preview",
"summary": "CRISPR interference Perturb-seq: filtered feature barcode matrix, raw feature barcode matrix, sparse gene count matrix, unfiltered global differential expression, unfiltered local differential expression"
},
"file_size": 673686640,
"gene_list_for": [],
"href": "/matrix-files/IGVFFI8767IWEB/@@download/IGVFFI8767IWEB.h5",
"input_file_for": [
"/matrix-files/IGVFFI3141VIGP/",
"/tabular-files/IGVFFI8786YBUA/",
"/tabular-files/IGVFFI4410YZQZ/"
],
"integrated_in": [],
"lab": {
"@id": "/labs/gary-hon/",
"title": "Gary Hon, UT"
},
"loci_list_for": [],
"md5sum": "306662b0bad1f1b4ccefc17c1690b049",
"principal_dimension": "cell",
"quality_metrics": [],
"reference_files": [
"/reference-files/IGVFFI6815WBWB/"
],
"s3_uri": "s3://igvf-files/2024/12/17/9afbd204-69be-4244-a9fe-fdc4f76e6723/IGVFFI8767IWEB.h5",
"schema_version": "7",
"secondary_dimensions": [
"UMI count"
],
"status": "preview",
"submitted_by": {
"@id": "/users/b05645f1-2d56-4a5e-b272-4601e555a3fa/",
"title": "Mpathi Nzima"
},
"submitted_file_name": "/project/GCRB/Hon_lab/s215194/Single_Cell/mini_cm_pilot_02_inducible/_435-438_WTC11_PB9/_aggr_transcriptome/cm_pilot_mini_02_no_normalization_WTC11_PB9/outs/count/filtered_feature_bc_matrix.h5",
"summary": "cell by UMI count in filtered feature barcode matrix",
"upload_status": "validated",
"uuid": "9afbd204-69be-4244-a9fe-fdc4f76e6723",
"workflow": {
"@id": "/workflows/IGVFWF0190YALU/",
"name": "Hon Perturb-seq Workflow",
"uniform_pipeline": false
}
}