|
| Status |
Public on May 02, 2020 |
| Title |
MCT treatment for 4 week (MCTW4) rep1 |
| Sample type |
SRA |
| |
|
| Source name |
lung tissue
|
| Organism |
Rattus norvegicus |
| Characteristics |
strain: Sprague-Dawley
tissue: lung
treatment: monocrotaline (MCT)
sacrifice time: sacrificed at week 4 after MCT treatment
|
| Treatment protocol |
PAH model in rats was induced by a single intraperitoneal injection of 40 mg/kg MCT. A total of 17 rats were used in this study, 12 rats were randomly assigned into 4 groups and treated with MCT (n = 3, each group). 5 remaining rats served as control and treated with saline.. Control and MCT-treated rats were sacrificed at week 0, 1, 2, 3 and 4.
|
| Growth protocol |
Sprague-Dawley rats, male and female rats, 200-250g, were raised and housed in the animal room and received food and water ad libitum.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Rat lungs were isolated and frozen in liquid nitrogen and then stored at -80°C after sacrifice.Total RNA was isolated from 50 mg lung tissues using 1 mL Trizol reagent following manufacturer’s instructions. RNA integrity and quality were assessed by gel electrophoresis and its concentration and purity were determined by the Thermo Scientific NanoDropTM instruments. Total RNA with high quality was used for cDNA library preparation.
Library preparation and RNA-seq were performed on an Illumina HiSeq 2000 platform by Genenergy Biotechnology (Shanghai) Co., Ltd.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
The quality of generated reads was assessed by FastQC software.
The low quality reads and adapter sequences were removed by Skewer software.
The alignment of clean reads to rat reference genome was performed using STAR software .
The transcripts were assembled by using the StringTie software.
The values of transcript expression in each sample were determined by HTSeq software throuth calculation of fragments per kilobase of transcript per million fragments mapped (FPKM).
Genome_build: Rn6
Supplementary_files_format_and_content: tab-delimited text files include read count values for each Sample
|
| |
|
| Submission date |
May 01, 2020 |
| Last update date |
May 07, 2020 |
| Contact name |
Genfa Xiao |
| E-mail(s) |
iesvev1986@aliyun.com
|
| Organization name |
First Affiliated Hospital of Fujian Medical University
|
| Lab |
Fujian hypertension research institute
|
| Street address |
chazhong road 20
|
| City |
Fuzhou |
| State/province |
Fujian |
| ZIP/Postal code |
350005 |
| Country |
China |
| |
|
| Platform ID |
GPL14844 |
| Series (1) |
| GSE149713 |
RNA sequencing analysis of monocrotaline-induced pulmonary arterial hypertension |
|
| Relations |
| BioSample |
SAMN14791390 |
| SRA |
SRX8241363 |
