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Unknown,Transcriptomics,Genomics,Proteomics

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Gene expression profiles of MBP-specific T cells during experimental autoimmune encephalomyelitis

ABSTRACT: 2nd generation sequencing was used to compare expression profiles of MBP-specific T cells retrieved from blood, CSF, spinal cord meninges and parenchyma. The overall expression profiles were found to be very similar.However, genes regulated during T cell activation were found to be upregulated in T cells from spinal cord meninges and parenchyma compared to blood and CSF. 2nd generation sequencing of MBP-specific T cells retrieved from blood and CNS compartments during experimental autoimmune encephalomyelitis

ORGANISM(S): Rattus norvegicus

SUBMITTER: Gabriela Salinas-Riester

PROVIDER: E-GEOD-75488 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Effector T-cell trafficking between the leptomeninges and the cerebrospinal fluid.

Schläger Christian C Körner Henrike H Krueger Martin M Vidoli Stefano S Haberl Michael M Mielke Dorothee D Brylla Elke E Issekutz Thomas T Cabañas Carlos C Nelson Peter J PJ Ziemssen Tjalf T Rohde Veit V Bechmann Ingo I Lodygin Dmitri D Odoardi Francesca F Flügel Alexander A

Nature 20160210 7590

In multiple sclerosis, brain-reactive T cells invade the central nervous system (CNS) and induce a self-destructive inflammatory process. T-cell infiltrates are not only found within the parenchyma and the meninges, but also in the cerebrospinal fluid (CSF) that bathes the entire CNS tissue. How the T cells reach the CSF, their functionality, and whether they traffic between the CSF and other CNS compartments remains hypothetical. Here we show that effector T cells enter the CSF from the leptome ...[more]

PMID: 26863192

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Gene expression profiles of MBP-specific T cells during experimental autoimmune encephalomyelitis

Project description:2nd generation sequencing was used to compare expression profiles of MBP-specific T cells retrieved from blood, CSF, spinal cord meninges and parenchyma. The overall expression profiles were found to be very similar.However, genes regulated during T cell activation were found to be upregulated in T cells from spinal cord meninges and parenchyma compared to blood and CSF.

2016-02-12 | GSE75488 | GEO

Decorin protects cardiac myocytes against simulated ischemia/reperfusion injury

Project description:Primary cardiac myocytes isolated from neonatal Wistar rats were cultured and simulated ischemia/reperfusion injury were conducted on them in the presence or absence of decorin. Decorin is a small leucin-rich proteoglycan, which has a cardiocytoprotective effect. The underlaying mechanism of this cardiocytoprotective phenomenon is unknown, therefore our aim was to investigate the changes in the mRNA expression between the decorin (3nM) treated and vehicle-treated control cells.

2020-12-31 | E-MTAB-9325 | biostudies-arrayexpress

Histone H3K4 trimethylation in rat peripheral nerve

Project description:ChIP-seq of H3K4me3 in rat peripheral nerve was used to identify transcription start sites associated with Schwann cell-expressed genes. The analysis was performed in injured and control nerve to identify injury-responsive changes in Schwann cells. H3K4me3 ChIP samples were prepared from rat sciatic nerve at 1 day post-transection using both the distal stump of the injured nerve and the contralateral (sham) nerve.

2016-08-01 | E-GEOD-84272 | biostudies-arrayexpress

H3K27me3 ChIP-seq in rat peripheral nerve

Project description:ChIP-seq of H3K27me3 in rat peripheral nerve was used to identify sites of polycomb repression associated with genes in Schwann cells, which constitute the majority of cells in peripheral nerve. H3K27me3 ChIP samples were prepared from rat sciatic nerve and then sequenced. Inputs for these ChIP samples have previously been submitted as samples GSM1541282 and GSM1541283 in Series GSE63103

2016-08-01 | E-GEOD-84265 | biostudies-arrayexpress

Cardiac miRNA expression changes induced by prediabetes

Project description:The aim of the experiment was the analysis of key molecular changes with an unbiased, transcriptomics-based approach in a prediabetes model. Small RNA sequencing analysis was applied to explore the expression changes resulted high-fat chow (supplemented with 40% lard) diet for 21 weeks and a single low dose of streptozotocin (20 mg/kg) treatment at week 4. Long-Evans rats were used in the present study. Left ventricular samples(n=6) of both prediabetic and control groups were analyzed.

2020-04-24 | E-MTAB-8204 | biostudies-arrayexpress

RNAseq timecourse of rat neurons at hours (0, 2, 4, 8, 16, and 24) after treatment with BDNF, with & without ATF4 knockdown

Project description:The purpose of the study was to determine the potential role of ATF4 in gene regulation by brain derived neurotrophic factor (BDNF). To achieve this, we compared gene regulation by BDNF in cultured rat hippocampal neurons with or without prior ATF4 knockdown with shRNA. We surveyed cultures after 0,2,4,8 and 16 hrs of exposure to BDNF.

2017-09-09 | E-MTAB-6046 | biostudies-arrayexpress

Obesity modulates cardiac microRNA expression and decreases expression of Foxp2

Project description:The aim of the experiment was to analyze key molecular changes using an unbiased, transcript-based approach in an experimental obesity model. Small expression RNA sequencing analysis was used to reveal expression changes. Male Long-Evans rats were given a control (CON) or high fat (20%) high sucrose (15%) diet (HFS) for 25 weeks. From week 16, the animals were injected. 0.25 mg · kg - 1 daily with selegiline (CON + S and HFS + S) or vehicle (CON, HFS). Left ventricular samples from all four groups (n = 4-5) were analyzed.

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Characterization of genome-wide transcriptional changes in liver and adipose tissues of ZDF (fa/fa) rats fed R-Î±-lipoic acid by next-generation sequencing

Project description:We report on the characterization of lipogenic tissue transcriptional networks that support physiological responses of obese rats to a lipid-lowering bioactive food compound, R-a-lipoic acid (LA). Nine-week old male ZDF (fa/fa) rats were fed a chow diet supplemented with 3 g LA per kg diet or pair fed for two weeks. At the end of the trial, high-quality RNA was extracted from the liver and epididymal fat and subjected to transcriptome analysis using RNA-Seq technology. Results showed a substantially higher number of differentially expressed genes (DEG, q â¤ 0.05 and absolute log2(fold change) â¥ 1) in liver (110 genes) vs. epididymal fat (10 genes). Most epididymal fat DEG were also differentially expressed in liver and shared directionality of change. Gene Ontology (GO) analysis of these transcripts revealed significant enrichment of GO categories related to immune response, stress response, lipid metabolism, and carboxylic acid metabolic processes. Of interest interferon-related genes involved in defense against microorganism and innate immune response were induced by LA. Lipid metabolism-related transcript changes observed in LA-fed animals included downregulation of lipogenic genes (Pnpla3, Pnpla5, Elov6, Acly, Gpam, and Aacs) and concomitant upregulation of short-, medium- and long-chain fatty acid metabolic processes (Acot1, Acot2, Acsf2, and Crat). Transcriptional changes were accompanied by the lowering of abdominal adiposity and blood triacylglycerol levels. We conclude that LA dietary supplementation induces prominent gene expression changes in liver in support of significant improvement of whole-body lipid status For each tissue and feed combination (liver/LA+, liver/LA-, adipose/LA+, and adipose/LA-) the transcriptome was sequenced with 4 biological replicates.

2014-01-08 | E-GEOD-50424 | biostudies-arrayexpress

Enhancer Analysis in Peripheral Nerve: ChIP-seq of H3K27ac in P15 sciatic nerve

Project description:ChIP-seq of H3K27ac in P15 sciatic nerve 1 H3K27ac ChIP sample, with respective input

2015-04-01 | E-GEOD-64971 | biostudies-arrayexpress

Methylation Changes in Soybean Early Maturation Seed Compartments Using LCM

Project description:What methylation changes are occurring in different compartments of early maturation stage seed largely remains unknown. To uncover the possible role of DNA methylation in different compartments of early maturation stage seed, we characterized the methylome of two major compartments in embryonic cotyledon: cotyledon abaxial parenchyma (EM-COT-ABPY) and cotyledon adaxial parenchyma (EM-COT-ADPY) using Illumina sequencing. Illumina sequencing of bisulfite-converted genomic DNA from cotyledon abaxial parenchyma (EM-COT-ABPY) and cotyledon adaxial parenchyma (EM-COT-ADPY) compartments.

2012-05-11 | E-GEOD-37893 | biostudies-arrayexpress

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