Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

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

ABSTRACT: 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.

ORGANISM(S): Mus musculus

PROVIDER: GSE136405 | GEO | 2020/11/12

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

RNA sequencing of ipsilateral cortex after transient focal ischemia in mice

Project description:We report the application of Illumina paired-end RNA-seq approach for transcriptome of brain tissue in mice. By removing sequence-dependent bias and amplification noise using UMI-tools. The mapped reads of each sample were assembled using StringTie. After the final transcriptome was generated, StringTie and edgeR was used to estimate the expression levels of all transcripts. By obtaining a total of million paired-end reads of sequence from cerebral cortex tissue, we generated transcriptome profiles of mouse ischemic cortex in sham, 24 h after focal ischemia, 28 d after focal ischemia, with or without neuron-specific knockdown of TIPARP, respectively. We found 2017 differentially expressed genes (DEGs) between Sham+AAV-SYN-shRNA-Con and tMCAO+AAV-SYN-shRNA-Con group, and 516 DEGs between tMCAO+AAV-SYN-shRNA-Con and tMCAO+AAV-SYN-shRNA-TIPARP group at 24 h after stroke. In addition, we found 487 DEGs between Sham+AAV-SYN-shRNA-Con and tMCAO+AAV-SYN-shRNA-Con group, and 192 DEGs between tMCAO+AAV-SYN-shRNA-Con and tMCAO+AAV-SYN-shRNA-TIPARP group at 28 d after stroke. This study provides a detailed analysis of the underlying mechanisms of neuron-specific knockdown of TIPARP in neuronal injury and long-term effect, with biologic replicates, generated by RNA-seq technology.

2022-05-22 | GSE131712 | GEO

Genome-wide identification of enhancer domains in the healthy and post-stroke mouse cortices

Project description:Genome-wide identification of enhancer domains in the healthy and post-stroke mouse cortices

| PRJNA559075 | ENA

Genome-wide identification of enhancer domains in the healthy and post-stroke mouse cortices

Project description:We report the identification of enhancer domains in sham and stroke mouse cerebral cortices by high-throughput profiling of H3K27Ac chromatin modification. A total of 35.4, 28.8 and 29.6 million reads were generated from chromatin immunoprecipitated DNA from sham, stroke and pooled input samples. This resulted in 55,571 peaks in sham and 56,110 peaks in stroke samples representing 50408 and 51,292 active regions, respectively. These active regions represent putative enhancer domains.

2020-11-12 | GSE135480 | GEO

RNA Sequencing of WT Chronic Stroke Infarcts vs. Contralateral Cortices

Project description:We conducted bulk RNA sequencing on infarcts collected from young adult (3-month-old) mice at 7 weeks after the distal middle cerebral artery occlusion + hypoxia stroke model and compared them to contralateral cortices. As expected, differential expression (DE) analysis revealed marked differences between infarcts and contralateral cortices: 3,930 upregulated and 2,869 downregulated genes. The most significantly upregulated genes, including Lpl, Spp1, Cd36, Mmp2, and Mmp19, and the most highly enriched genes, including Cd5l, Mmp3, Mmp12, and Mmp13, indicate a pronounced disturbance in lipid homeostasis in infarcts at 7 weeks after stroke. In addition to alterations in lipid metabolic processes, the transcriptome also revealed a signature of chronic inflammation at 7 weeks after stroke. We then used IPA software to define upstream regulators and identify altered biological processes based on DE analysis. Differentially expressed genes were associated with the following upregulated biological processes: (i) atherosclerosis signaling, (ii) IL-1 signaling, (iii) inflammasome pathway, (iv) eicosanoid signaling, (v) B cell receptor (BCR) signaling, and (vi) phospholipases, along with others. IPA also identified lipid metabolic upstream regulators such as cholesterol, phospholipids, and LDL, as well as immunological upstream regulators such as MYD88, IL18, CD3, IL1B, TLR4, and TNF. These altered biological processes indicate that the stroke infarct transcriptome is characterized by chronic inflammation, dysregulated lipid metabolism, and impaired or absent neuronal function at 7 weeks after stroke.

2021-04-30 | GSE173544 | GEO

gut metagenome

Project description:Post stroke Depression Microbiome

| PRJNA493294 | ENA

The critical role of chondroitin sulfate proteoglycan interactions with receptor PTPσ in the inhibition of neural repair after stroke

Project description:We used RNAseq to compare transcriptome of peri-infarct cortex in stroke mice that received vehicle or ISP treatment (which blocks the PTPsigma receptor signaling) at 14 days post stroke. The purpose of this project is to identify genes that are differentially expressed in control stroke mice and ISP treated stroke mice that might mediated the behavioral improvement in ISP treated stroke mice.

2021-03-16 | GSE168934 | GEO

RNA Sequencing of WT Chronic Stroke Infarcts vs. Contralateral Cortices

Project description:RNA Sequencing of WT Chronic Stroke Infarcts vs. Contralateral Cortices

| PRJNA726051 | ENA

RNA sequencing facilitates quantitative analysis of siRNA circHIPK2 transfected neural stem cells and siRNA circCon transfected neural stem cells transcriptomes

Project description:We report the application of Illumina paired-end RNA-seq approach for transcriptome of siRNA circHIPK2 transfected neural stem cells and siRNA circCon transfected neural stem cells . By removing sequence-dependent bias and amplification noise using UMI-tools. The mapped reads of each sample were assembled using StringTie. After the final transcriptome was generated, StringTie and edgeR was used to estimate the expression levels of all transcripts. By obtaining a total of million paired-end reads of sequence from neural stem cells , we generated transcriptome profiles of siRNA circHIPK2 transfected neural stem cells and siRNA circCon transfected neural stem cells , respectively. We found 201 differentially expressed genes (DEGs) between siRNA circHIPK2 transfected neural stem cells and siRNA circCon transfected neural stem cells. This study provides a detailed analysis of the underlying mechanisms of stroke，such as neuronal injury and long-term effect, generated by RNA-seq technology.

2020-02-24 | GSE133701 | GEO

Comparing the Transcriptomes of Wild Type and Zp3-Cre mediated Mtor-Oocyte-Conditional Knockout (CKO) Mouse Metaphase II oocytes by RNA-Seq Analysis

Project description:The goal of this study is to identify the differentially expressed genes in Zp3-Cre mediated Mtor oocyte-specific knockout (CKO) Metaphase II (MII) oocytes by comparing the transcriptomes of Wild-Type (WT) and CKO Mouse MII oocytes via RNA-Seq Analysis. Methods: mRNA profiles of 3 sets of super-ovulated MII oocytes collected from 24-day old WT- and Mtor CKO female mice were generated by deep sequencing using an Illumina Hiseq2500 platform with 41bp single read. All RNA-seq reads passed filter were trimmed to remove low-quality bases and adaptor sequences. Reads then were aligned to the mm10 reference genome using tophat2 (v2.0.8b). Reads aligned to genes are counted by cufflinks (v2.1.1). The FPKMs are normalized usingcuffnorm. Differentially expressed genes are calculated using cuffdiff.

2021-05-01 | GSE98548 | GEO

Transfer RNA fragments replace microRNA regulators of the cholinergic post-stroke immune blockade III

Project description:After ischemic stroke, the brain initiates intensive communication with the immune system, and acetylcholine contributes to this process. Stroke triggers peripheral immunosuppression leading to increased susceptibility to infections; and post-stroke pneumonia is linked with poor stroke outcome, but the responsible processes are yet unknown. We discovered a “change of guards” where microRNA levels decreased but small transfer RNA fragments (tRFs) accumulated in post-stroke blood cells. This molecular switch may re-balance acetylcholine signaling in CD14+ monocytes by regulating their gene expression and modulating post-stroke immunity. Our observations point to tRFs as new molecular regulators of post-stroke immune responses that may become potential therapeutic targets.

2020-12-31 | GSE158313 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data