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Series GSE136405 Query DataSets for GSE136405
Status Public on Nov 12, 2020
Title Gene expression changes following Knock-down of eRNA_06347 in post-stroke mouse cortex
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary 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 final 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.
Overall design Genome-wide transcriptomic profiles of eRNA_06347 knockdown post-stroke mouse cortices compared to sham cortices and negative control post-stroke mouse cortices
Contributor(s) Dharap A, Bhattarai S, Akella A
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Submission date Aug 27, 2019
Last update date Nov 12, 2020
Contact name Ashutosh Dharap
Organization name HackensackMeridian Health JFK Medical Center
Department Neuroscience
Lab Laboratory for Stroke Research and Noncoding RNA Biology
Street address 65 James st
City Edison
State/province NJ
ZIP/Postal code 08820
Country USA
Platforms (2)
GPL19057 Illumina NextSeq 500 (Mus musculus)
GPL24247 Illumina NovaSeq 6000 (Mus musculus)
Samples (9)
GSM4048286 Sham1
GSM4048287 Sham2
GSM4048288 Sham3
BioProject PRJNA562512
SRA SRP219749

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Supplementary file Size Download File type/resource
GSE136405_RAW.tar 126.6 Mb (http)(custom) TAR (of GTF)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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