|
| Status |
Public on Jan 19, 2024 |
| Title |
scRNA_HT_Scr1 |
| Sample type |
SRA |
| |
|
| Source name |
Human Umbilical Vein Endothelial Cells transfected with scramble LNA, 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 scramble LNA, treated with 25mM glucose + 5ng/ml TNFa and harvested after 72 hours
assay: scRNA-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
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
Single-cell 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.
|
| |
|
| 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 |
SAMN30478991 |
| SRA |
SRX17239401 |
