|
| Status |
Public on Jan 19, 2024 |
| Title |
HUVEC_NM_SncKD1 |
| Sample type |
SRA |
| |
|
| Source name |
Human Umbilical Vein Endothelial Cells transfected with LNA targeting SncmtRNA, treated with normal glucose + 25mM mannitol 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 normal glucose + 25mM mannitol and harvested after 72 hours
assay: RNA-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 NM or HT conditions and then harvested after 72 hours post transfection for SncmtRNA knockdown experiments. Alternatively, HUVECs were infected with AAV expressing Tdtomato (Ctrl) or SncmtRNA (SncOE) and collected after 72 hours for SncmtRNA overexpression experiments.
|
| Growth protocol |
HUVECs were cultured following the manufacturer's protocol
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Approximately 1 million cells were used for total RNA extraction and construction of strand-specific mRNA-seq library
The libraries were constructed using the KAPA mRNA stranded Hyper kit following the user manual
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
polyA RNA enriched
|
| Data processing |
Adaptors were timmed by Trimmomatic-0.39
Trimmed data was aligned to hg38 with STAR(2.7.10a)
reads map to genomic features were counted by FeatureCounts
Assembly: hg38
Supplementary files format and content: The processed counts.txt files are tab-delimited tables which includes annotation columns (‘Geneid’) and data columns (i.e. read counts for genes) for each library.
|
| |
|
| 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) |
| GSE211969 |
Regulation of nuclear transcription by mitochondrial RNAs [bulkRNA-seq] |
| GSE211971 |
Regulation of nuclear transcription by mitochondrial RNAs |
|
| Relations |
| BioSample |
SAMN30478969 |
| SRA |
SRX17238252 |
