|
| Status |
Public on Apr 25, 2019 |
| Title |
Fetal hypoxia RNAseq 3 |
| Sample type |
SRA |
| |
|
| Source name |
Heart
|
| Organism |
Rattus norvegicus |
| Characteristics |
strain: Sprague Dawley
tissue: heart
age: E21
treatment: hypoxia
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from heart tissue using TRIzol RNA Isolation reagent. Briefly, each solid tissue was homogenized in 1 mL TRIzol and the lysate was then extracted with chloroform and centrifuged at 14 000 rpm for 15 min at 4°C. Finally, total RNA was precipitated and washed thoroughly with 70% ethanol, airdried and reconstituted in nuclease free water. RNA quality was assessed using the 2200 TapeStation. Heart samples had an average RIN number of 9.5.
RNA-seq libraries were constructed using the Ovation Universal RNAseq System.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 550 |
| |
|
| Description |
fetal_gene_fpkm.csv
H5-3
|
| Data processing |
Illumina Casava1.8 software used for basecalling.
Hard trimming and adaptor trimming were performed by Trimmomatic v0.35. The trimmed reads were aligned to the rat reference genome NCBI Rnor6.0 with TopHat v2.1.1 with default parameter settings.
The aligned bam files were then processed using Cufflinks v2.2.1 for gene quantification.
The gene expression profiles (Fragments Per Kilo base per Million or FPKM) were used as the input for differential expression gene (DEG) analysis by using Cuffdiff. Differential expressed genes were based on FDR < 0.3 and fold change (FC) > 1.2.
Genome_build: Rnor6.0
|
| |
|
| Submission date |
Apr 15, 2019 |
| Last update date |
Apr 25, 2019 |
| Contact name |
Charles Wang |
| E-mail(s) |
[email protected]
|
| Organization name |
Loma Linda University
|
| Street address |
11021 Campus St
|
| City |
Loma Linda |
| State/province |
CA |
| ZIP/Postal code |
92350 |
| Country |
USA |
| |
|
| Platform ID |
GPL25029 |
| Series (2) |
| GSE129848 |
Prenatal hypoxia exposure induced methylomic and transcriptomic alterations in rat hearts [RNA-seq] |
| GSE129876 |
Prenatal hypoxia exposure induced methylomic and transcriptomic alterations in rat hearts |
|
| Relations |
| BioSample |
SAMN11433309 |
| SRA |
SRX5693623 |
