|
| Status |
Public on Jul 18, 2018 |
| Title |
gaotang12 |
| Sample type |
SRA |
| |
|
| Source name |
Human retinal endothelial cells (hRECs)
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Human retinal endothelial cells (hRECs)
treatment: high glucose
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were collected and total RNAs were extracted from hRECs, using TRIzol reagent (Takara, Dalian, China), according to the manufacturer's instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Description |
Human retinal endothelial cells (hRECs) from passage 4 were diluted to 8×104/mL and incubated in 6-well plates with low glucose (LG) media until confluent. After washing with PBS, the cells were further cultured for 48 h at 37 °C in low glucose (LG), high glucose (HG), or high glucose with 4 uM TTR (HG+TTR) media.
|
| Data processing |
Raw reads were trimmed using Skewer, then mapped to GRCh38.90 whole genome using STAR verison 2.5.2b with parameters --twopassMode Basic --outSAMstrandField intronMotif --alignSJstitchMismatchNmax 5 -1 5 5
Transcripts were assembled by StringTie, FPKM and raw read counts were calculated using ballgown
DESeq2 was used for all differential expression analysis from the raw read counts
Genome_build: GRCh38.90
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample
|
| |
|
| Submission date |
Jul 17, 2018 |
| Last update date |
Jul 18, 2018 |
| Contact name |
Yunbin Zhang |
| Organization name |
Chinese Academy of Sciences
|
| Department |
Shanghai Institute of Biochemistry and Cell Biology
|
| Street address |
No. 320, Yueyang Road, Xuhui District
|
| City |
Shanghai |
| ZIP/Postal code |
200031 |
| Country |
China |
| |
|
| Platform ID |
GPL21290 |
| Series (1) |
| GSE117238 |
Transcriptome profiling identified a 3-lncRNA regulatory network in transthyretin against glucose induced hRECs dysfunction |
|
| Relations |
| BioSample |
SAMN09671188 |
| SRA |
SRX4400356 |
