|
| Status |
Public on Aug 16, 2021 |
| Title |
P21_volume_2 |
| Sample type |
SRA |
| |
|
| Source name |
RV free wall myocardium
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: myocardium
treatment method: volume overload(AVF)
treatment age: postnatal day 7
test age: postnatal day 21
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Myocardium of RV free wall was rapidly removed from executed mice and flash frozen in -80℃ refrigerator , RNA was harvested using Trizol reagent.
A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
The mapped reads of each sample were assembled by StringTie (v1.3.3b) (Mihaela Pertea.et al. 2015) in a reference-based approach.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.16.1).
Gene Ontology (GO) enrichment analysis of differentially expressed genes was implemented by the clusterProfiler R package, in which gene length bias wascorrected.We used clusterProfiler R package to test the statistical enrichment of differential expression genes in KEGG pathways.
GATK2 (v3.7) software was used to perform SNP calling. Raw vcf files were filtered with GATK standard filter method and other parameters (cluster:3; WindowSize:35; QD < 2.0 o; FS > 30.0; DP < 10 and SnpEff software was used to annotation for the Variablesite.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.16.1).
Alternative Splicing is an important mechanism for regulate the expression of genes and the variable of protein. rMATS(3.2.5) software was used to analysis the AS event.
PPI analysis of differentially expressed genes was based on the STRING database, which known and predicted Protein-Protein Interactions.
WGCNA (Weighted correlation network analysis) was used to describe the gene association modes among different samples.
Genome_build: GRCm38(mm10)
Supplementary_files_format_and_content: FPKM
|
| |
|
| Submission date |
Sep 03, 2020 |
| Last update date |
Aug 16, 2021 |
| Contact name |
Sijuan Sun |
| E-mail(s) |
silkssj@alumni.sjtu.edu.cn
|
| Phone |
86-13636478725
|
| Organization name |
Shanghai Children’s Medical Center (SCMC) affiliated to Shanghai Jiaotong University School of Medicine
|
| Street address |
No.1678, Dongfang Road
|
| City |
Shanghai |
| ZIP/Postal code |
200127 |
| Country |
China |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE157396 |
Time dependence of volume overload on right ventricular remodeling during preadolescence |
|
| Relations |
| BioSample |
SAMN16047927 |
| SRA |
SRX9066482 |
