|
| Status |
Public on Nov 09, 2023 |
| Title |
Hypoxia siRNA-KMT2E-AS1 2 |
| Sample type |
SRA |
| |
|
| Source name |
Pulmonary arterial endothelial cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Pulmonary arterial endothelial cells
treatment: siRNA KMT2E-AS1+0.2% oxygen
time: 8 hour siRNA incubation then hypoxia 0.2% oxygen the following day for 24 hours
|
| Treatment protocol |
Cultured HPAECs were transfected with siRNAs targeting either negative control, KMT2E-AS1 or KMT2E, then exposed to hypoxic stress (0.2% oxygen) for 24 hours.
|
| Growth protocol |
Primary HPAECs were grown in EBM-2 basal medium supplemented with EGM-2 MV BulletKit (Lonza).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were harvested for total RNA extraction using Rneasy mini kit (Qiagen) with DNase digestion (Qiagen).
Illumina stranded total RNA library was prepared for the RNA sequencing. mRNA and lncRNA profiles were generated by deep sequencing, using NextSeq 2000 P3 flow cell (2 x 101bp, 40M reads/sample).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 2000 |
| |
|
| Description |
Hx_siAS_2_S8
|
| Data processing |
The raw fastq reads were mapped against the human genome build hg19 using STAR aligner.
The read counts for each gene were calculated using featureCounts.
Gene expression was normalized by DESeq2 with variance-stabilizing transformation (VST).
The low expression genes with total counts across all samples less than 10 were excluded.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include raw count values for each sample
|
| |
|
| Submission date |
May 18, 2023 |
| Last update date |
Nov 09, 2023 |
| Contact name |
Satoshi Okawa |
| E-mail(s) |
okawas@pitt.edu
|
| Organization name |
University of Pittsburgh
|
| Street address |
200 Lothrop Street
|
| City |
Pittsburgh |
| State/province |
PA |
| ZIP/Postal code |
15261 |
| Country |
USA |
| |
|
| Platform ID |
GPL30173 |
| Series (2) |
| GSE232797 |
mRNA and lncRNA profiling of hypoxic human pulmonary artery endothelial cells treated with siRNA-mediated knockdown of KMT2E-AS1 or KMT2E |
| GSE232799 |
H3K4me3, mRNA and lncRNA profiling of hypoxic human pulmonary artery endothelial cells treated with KMT2E-AS1 siRNA |
|
| Relations |
| BioSample |
SAMN35159530 |
| SRA |
SRX20431073 |
