Unknown,Transcriptomics,Genomics,Proteomics

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The identification of circular RNAs from peripheral blood mononuclear cells in systemic lupus erythematosus

ABSTRACT: Total RNA from each sample was quantified using the NanoDrop ND-1000. The sample preparation and microarray hybridization were performed based on the Arraystar’s standard protocols. Briefly, total RNA from each sample was amplified and transcribed into fluorescent cRNA utilizing random primer according to Arraystar’s Super RNA Labeling protocol (Arraystar Inc.). The labeled cRNAs were hybridized onto the Arraystar Human circRNA Array (6x7K, Arraystar). After having washed the slides, the arrays were scanned by the Axon GenePix 4000B microarray scanner.

ORGANISM(S): Homo sapiens

SUBMITTER: penny cheng

PROVIDER: E-MTAB-10125 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:We conducted a microarray study of sigmoid mucosal gene expression in pilot sample of Rome III+ IBS patients and age and sex-matched HCs. This sample was balanced by sex, free of active psychiatric disease and had limited use of medications. Rome III+ IBS patients and HCs ages 18-55 were recruited primarily by community advertisement. Bowel habit subtypes (IBS with diarrhea (IBS-D), constipation (IBS-C) and mixed pattern (IBS-M)) were based on the Rome III criteria. The diagnosis was confirmed by a clinician with expertise in IBS. Rome III+a IBS patients and HCs ages 18-55 were recruited primarily by community advertisement. Bowel habit subtypes (IBS with diarrhea (IBS-D), constipation (IBS-C) and mixed pattern (IBS-M)) were based on the Rome III criteria. The diagnosis was confirmed by a clinician with expertise in IBS. HCs had no personal or family history of IBS or other chronic pain conditions. Additional exclusion criteria for all subjects included: infectious or inflammatory disorders, active psychiatric illness over the past 6 months as assessed by structured clinical interview for the DSM-IV (MINI),b use of corticosteroids in the past six months, use of narcotics, antidepressants or other medications that could affect neuroendocrine function in the past two months, or current tobacco or alcohol abuse. Participants were compensated. Our goal was to evaluate women during the follicular phase or days 4-14 of their menstrual cycle if on oral contraceptive pills. Phase was determined by date of last menstrual period and progesterone levels. The study was approved by the UCLA Institutional Review Board, and all subjects signed a written informed consent prior to start of study. IBS symptom severity over the prior week was assessed with a numeric rating scale (0-20).c Current anxiety and depression symptoms were measured with the Hospital Anxiety and Depression (HAD) scale.d Sigmoid biopsies (30cm from the anal verge) were obtained by flexible sigmoidoscopy following tap water enemas. Specimens were immediately flash frozen in liquid nitrogen. RNA was extracted with TRIzol. Sigmoid biopsies (30cm from the anal verge) were obtained by flexible sigmoidoscopy following tap water enemas. Specimens were immediately flash frozen in liquid nitrogen. Differential expression analysis was done on mRNA only (\\ormalized_Unfiltered_mRNAonly.txt\\) using limma[1]. Weighted gene coexpression network analysis (WGCNA[2]) was done using all targets after removing those on X and Y chromosomes and filtered by mean raw signal >200. 1. Smyth GK. Linear models and empirical bayes methods for assessing differential expression in microarray experiments. Stat Appl Genet Mol Biol. 2004;3:Article3. 2. Langfelder P, Horvath S. WGCNA: an R package for weighted correlation network analysis. BMC Bioinformatics. 2008;9:559.\

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The identification of circular RNAs from peripheral blood mononuclear cells in systemic lupus erythematosus

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