|
| Status |
Public on Dec 17, 2020 |
| Title |
Chronc hypoxia 1 |
| Sample type |
SRA |
| |
|
| Source name |
heart
|
| Organism |
Rattus norvegicus |
| Characteristics |
strain: Sprague Dawley
tissue: heart
age: Three months
treatment: Chronic hypoxia
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Heart tissues from hypoxic (n = 4) and normoxic rats (n = 4) were collected for RNA extraction. Total RNA was extracted by Trizol™ Reagent (no. 15596018, Thermo Fisher Scientific, USA) following the manufacturer’s protocol.
The sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (no. E7530L, NEB, USA) following the manufacturer’s recommendations and index codes were added to attribute sequences to each sample. The clustering of the index-coded samples was performed on a cBot cluster generation system using HiSeq PE Cluster Kit v4-cBot-HS (Illumina, USA) according to the manufacturer’s instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
| |
|
| Data processing |
bcl2fastq software was used for basecalling
In order to guarantee the data quality which was used to analysis, the useful Perl script was used to filter the Raw Data. The steps are:(1) Trim Smart-seq2 public primer sequence from the Reads;(2) Remove the contaminated reads for adapters; (3) Remove the low quality reads;(4) Remove the reads whose N base is more than 5% for total bases
The reference genomes and the annotation file were downloaded from ENSEMBL database (http://www.ensembl.org/index.html). Bowtie2 v2.2.3 was used for building the genome index, and Clean Data was then aligned to the reference genome using HISAT2 v2.1.0.
Reads Count for each gene in each sample was counted by HTSeq v0.6.0, and FPKM was then calculated to estimate the expression level of genes in each sample
Genome_build: rn6
Supplementary_files_format_and_content: tab-delimited text files include Counts and FPKM values for each Sample
|
| |
|
| Submission date |
Dec 17, 2018 |
| Last update date |
Dec 17, 2020 |
| Contact name |
Yiwei Liu |
| E-mail(s) |
jacklyw@foxmail.com
|
| Organization name |
fuwai hosptial, PUMC & CAMS
|
| Department |
Pediatric Cardiac Surgery
|
| Lab |
State Key Laboratory of Cardiovascular Disease
|
| Street address |
No.167 North Lishi Road, Xicheng District
|
| City |
Beijing |
| ZIP/Postal code |
100037 |
| Country |
China |
| |
|
| Platform ID |
GPL24688 |
| Series (1) |
| GSE123948 |
The Effect of Chronic Hypoxia on Cardiac Gene Expression in Rattus Norvegicus |
|
| Relations |
| BioSample |
SAMN10602937 |
| SRA |
SRX5141083 |
