{
"@context": "/terms/",
"@id": "/matrix-files/IGVFFI5439VMRC/",
"@type": [
"MatrixFile",
"File",
"Item"
],
"accession": "IGVFFI5439VMRC",
"aliases": [
"gary-hon:WTC11_CM_Pilot2_Mini_LPv4_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 [IGVFFI5439VMRC](/matrix-files/IGVFFI5439VMRC/) 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/IGVFFI5439VMRC/"
}
]
},
"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": "2024-12-17T23:42:37.689714+00:00",
"file_format": "hdf5",
"file_set": {
"@id": "/analysis-sets/IGVFDS5498SDRJ/",
"accession": "IGVFDS5498SDRJ",
"file_set_type": "principal analysis",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM7766HOYF/",
"accession": "IGVFSM7766HOYF",
"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": "GM25256 (WTC-11) differentiated cell specimen induced to cardiac muscle cell for 12 days (cellular sub pool: subpool_LW429), male, Homo sapiens modified with CRISPRi Sp-dCas9, transduced (lentivirus) 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/IGVFSM0565MLZG/",
"accession": "IGVFSM0565MLZG",
"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": "GM25256 (WTC-11) differentiated cell specimen induced to cardiac muscle cell for 12 days (cellular sub pool: subpool_LW427), male, Homo sapiens modified with CRISPRi Sp-dCas9, transduced (lentivirus) 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/IGVFSM2127MVQH/",
"accession": "IGVFSM2127MVQH",
"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": "GM25256 (WTC-11) differentiated cell specimen induced to cardiac muscle cell for 12 days (cellular sub pool: subpool_LW430), male, Homo sapiens modified with CRISPRi Sp-dCas9, transduced (lentivirus) 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/IGVFSM9285BBSI/",
"accession": "IGVFSM9285BBSI",
"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": "GM25256 (WTC-11) differentiated cell specimen induced to cardiac muscle cell for 12 days (cellular sub pool: subpool_LW428), male, Homo sapiens modified with CRISPRi Sp-dCas9, transduced (lentivirus) 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/",
"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": "GM25256 (WTC-11) differentiated cell specimen induced to cardiac muscle cell for 12 days (cellular sub pool: subpool_LW438), male, Homo sapiens modified with CRISPRi Sp-dCas9, transfected 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": "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": 767591830,
"gene_list_for": [],
"href": "/matrix-files/IGVFFI5439VMRC/@@download/IGVFFI5439VMRC.h5",
"input_file_for": [],
"integrated_in": [],
"lab": {
"@id": "/labs/gary-hon/",
"title": "Gary Hon, UT"
},
"loci_list_for": [],
"md5sum": "224f65691185c8c84cb63e3cc4f2f53e",
"principal_dimension": "cell",
"reference_files": [
"/reference-files/IGVFFI6815WBWB/"
],
"s3_uri": "s3://igvf-files/2024/12/17/c6c23dfa-2e3d-4e90-8698-a33af425b1ef/IGVFFI5439VMRC.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/_427-430_Lpv4/_aggr_transcriptome/cm_pilot_mini_02_no_normalization_LPv4/outs/count/filtered_feature_bc_matrix.h5",
"summary": "cell by UMI count in filtered feature barcode matrix",
"upload_status": "validated",
"uuid": "c6c23dfa-2e3d-4e90-8698-a33af425b1ef"
}