Pluto Bioinformatics

GSE136405: Gene expression changes following Knock-down of eRNA_06347 in post-stroke mouse cortex

Bulk RNA sequencing

RNA-sequencing was conducted to profile the transcriptome of the eRNA_06347 knockdown post-stroke mouse cortices ( knockdown achieved by intracerebroventricular injection of oligos against eRNA_06347). RNA was isolated from sham, Negative control oligo injected post-stroke cortices and eRNA_06347 knockown post-stroke cortices (three independent biological replicates per group),converted into cDNA libraries, and used for Illumina deep sequencing.The sequencing reads were aligned to the mouse reference genome GRCm38 using HISAT2. Stringtie was used to assemble the aligned sequences into transcript isoforms using mouse transcript annotations from Ensembl 81 as a guide, then merged to reconstruct a comprehensive transcriptome using perl scripts and gffcompare. After the nal transcriptome was generated, StringTie and Ballgown were used to estimate the expression levels of all the transcripts. StringTie was used to evaluate expression levels for mRNAs by calculating the FPKMs. The differentially expressed mRNAs were identified as log2 fold change >1 or log2 fold change <-1 and with statistical significance p<0.05 using Ballgown.Doing so, We found that 106 genes were significantly upregulated and 49 genes were significantly downregulated in the eRNA_06347 knockdown group as compared to the negative control. SOURCE: Ashutosh Dharap ( - Laboratory for Stroke Research and Noncoding RNA Biology HackensackMeridian Health JFK Medical Center

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