|
| Status |
Public on Feb 25, 2016 |
| Title |
normal cells |
| Sample type |
SRA |
| |
|
| Source name |
endothelial cells_control
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: umbilical vein
cell type: endothelial cells
passage: 15-18
|
| Treatment protocol |
HUVECs were treated with 400μmol H2O2 diluted with medium for 24h.
|
| Growth protocol |
HUVECs were incubated with medium in a humidified atmosphere of 95% air and 5% CO2. Medium was changed every 48 hours until the cells were grown to 80 to 90% confluency.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from each sample was extracted using TRK1001 (LC Sciences, Cat. TRK-1001, Total RNA Purification Kit) according to the manufacturer's procedure. Total RNA was quantified by the NanoDrop ND-2000 (Thermo Scientific) and the RNA integrity was assessed using Agilent Bioanalyzer 2100 (Agilent Technologies).
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
Normal culture
|
| Data processing |
All obtained reads from each sample were mapped against the human genome (hg19 build) with Bowtie/Tophat v2.0.2 which allows mapping across splice sites by reads segmentation (Trapnell et al., 2012). All programs were performed with default setting (unless otherwise specified).
The unique mapped reads (85-90% of total reads) were subsequently assembled into transcripts guided by reference annotation (Gencode v20 and Refseq gene models) with Cufflinks v2.0.2 (Trapnell et al., 2012). Expression level of each gene was quantified with normalized FPKM (fragments per kilobase of exon per million mapped fragments).
For the analyses of lncRNAs, cufflinks was used to estimate the transcript level FPKM values with the Gencode v20 lincRNA annotation (Derrien et al., 2012), and human body map lincRNA annotations (Cabili et al., 2011).
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample
|
| |
|
| Submission date |
Feb 24, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Rui Zhang |
| E-mail(s) |
ydyyzxsys@163.com
|
| Phone |
0311-85917258
|
| Organization name |
The First Hospital of Hebei Medical University
|
| Street address |
No.89, Donggang Road
|
| City |
Shijiazhuang |
| ZIP/Postal code |
050031 |
| Country |
China |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE78275 |
Oxidative stress related long non-coding RNAs (lncRNAs) in human umbilical vein endothelial cells |
|
| Relations |
| Reanalyzed by |
GSE81474 |
| BioSample |
SAMN04514958 |
| SRA |
SRX1598978 |
