|
Status |
Public on Jan 19, 2024 |
Title |
snRNA_HT_SncKD2 |
Sample type |
SRA |
|
|
Source name |
Human Umbilical Vein Endothelial Cells transfected with LNA targeting SncmtRNA, treated with 25mM glucose + 5ng/ml TNFa and harvested after 72 hours
|
Organism |
Homo sapiens |
Characteristics |
cell line: HUVEC cell type: Human Umbilical Vein Endothelial Cells treatment: transfected with LNA targeting SncmtRNA, treated with 25mM glucose + 5ng/ml TNFa and harvested after 72 hours assay: snRNA-seq
|
Treatment protocol |
HUVECs were cultured in complete medium; transfected with either 20 nM scramble LNA (Scr) or 10nM LNA targeting SncmtRNA (Snc-KD) under HT conditions and then harvested after 72 hours post transfection.
|
Growth protocol |
HUVECs were cultured following the manufacturer's protocol
|
Extracted molecule |
polyA RNA |
Extraction protocol |
Single-cell suspension was prepared by using the 10XGenomics Chromium Controller 10X Genomics Single Cell 3' v3.1. gene expression
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|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic single cell |
Library selection |
cDNA |
Instrument model |
Illumina NovaSeq 6000 |
|
|
Description |
Single-nuclear RNA sequencing assay
|
Data processing |
10X Genomics cellranger (v3.1) was used to process sequencing data produced from Chromium Single Cell Gene Expression Seurat 4.0 was used to analyze the scRNA-seq data Assembly: hg38 Supplementary files format and content: Three processed data files per each sample: a matrix file (.mtx format) with UMI counts per each gene (rows) and single cell (columns); genes list (.tsv format) with the list of genes (features) detected; cell barcodes list (.tsv format) with the list of barcodes of the single cells in the sample.
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|
|
Submission date |
Aug 24, 2022 |
Last update date |
Jan 19, 2024 |
Contact name |
Zhen Chen |
E-mail(s) |
zhenchenlab@gmail.com
|
Organization name |
City of Hope
|
Department |
DMRI
|
Street address |
1500 E Duarte Rd
|
City |
Duarte |
State/province |
CA |
ZIP/Postal code |
91010 |
Country |
USA |
|
|
Platform ID |
GPL24676 |
Series (2) |
GSE211970 |
Regulation of nuclear transcription by mitochondrial RNAs [scRNA-seq/snRNA-seq] |
GSE211971 |
Regulation of nuclear transcription by mitochondrial RNAs |
|
Relations |
BioSample |
SAMN30478992 |
SRA |
SRX17239400 |