Effect of depletion of C10orf71 on gene expression in hearts from embryonic mice at E18.5 and adult mice
Ontology highlight
ABSTRACT: To explore the specific functional and cellular processes that affected by the mC10orf71 deletion, we compared total RNA expression in hearts from E18.5. Gene Ontology (GO) enrichment analysis showed that down-regulated genes were not significantly enriched in any biological process. The 327 genes up-regulated in KO mice were enriched for energy generation, electron transport chain and ATP synthesis, and many of them are encoded by mitochondrial DNA. These changes were likely to be a compensatory response to the impaired morphogenesis and dysfunction of the KO hearts. Then, we performed RNA-seq on hearts of adult WT and KO mice. GO analysis of down-regulated genes identified two categories of biological processes: mRNA processing/splicing and muscle cell differentiation/contraction.
Project description:Purpose: The goal of this study is to compare the cardiac transcriptome profiling (RNA-seq) of WT and CHD4-M195I hearts at E18.5 to conclude genes affected by this CHD4 mutation. Methods: mRNA profiles of E18.5 WT and CHD4-M195I mouse hearts were generated by deep sequencing, n=4 for each genotype, using Illumina HiSeq2500. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks. Results: RNA-sequencing (RNA-seq) analyses on E18.5 WT and CHD4-M195I hearts and identified 323 genes that were differentially expressed [adjusted P value <0.05, |log2(Fold Change)| > 0.5], 113 upregulated and 210 downregulated in CHD4-M195I hearts.
Project description:Microarray experiment to identify changes in gene expression in 18.5 day post coitum Tex19.1-/- mouse placenta. Tex19.1 is expressed in trophectoderm-derived cells in the placenta. Tex19.1-/- placentas are small and have defects in junctional zone and labyrinth layers of the placenta, Tex19.1-/- embryos exhibit intra-uterine growth retardation. Data provides insight into the changes in gene expression and cell composition in Tex19.1-/- placentas. Six E18.5 Tex19.1-/- placentas (KO: four XX, two XY), four E18.5 Tex19.1+/- littermate control placentas (HET: four XX), and two E18.5 Tex19.1+/+ littermate control placentas (WT: two XY) are included in the analysis.
Project description:Comparisons of placenta gene expression profiles of BAHD1-KO mice to those of wild-type littermate mice. We used DNA microarrays to identify the repertoire of genes differentially expressed by ablation of the BAHD1 gene in the placenta at embryonic day E18.5
Project description:To further explore the mechanism of SYISL knockout on muscle fiber development, we performed 10X Genomics single-cell RNA sequencing of leg muscles from E18.5-day WT and KO fetal mice from the same litter.
Project description:To assess the requirement of Ptbp2 for alternative mRNA expression in mouse brain RNA from the cortex of 4 wild type and 4 Ptbp2 KO E18.5 mice. One array per sample (biological replicate), 8 arrays total.
Project description:Analysis of genes regulated by Tshz1 in olfactory bulb neurons. Total RNA from olfactory bulbs of embryonic day E18.5 and postnatal day 30 control mice was compared to Tshz1 mutant mice
Project description:MafB is a member of the Maf family of bZip transcription factor and plays important roles in the developmental processes of various tissues, as well as in cell-type specific gene expression. MafB is expressed in differentiating keratinocytes in mice and is transcriptionally up-regulated upon human keratinocyte differentiation in vitro. In MafB-deficient mice, epidermal differentiation is partially impaired and the cornified layer is thinner. To gain insights into more detailed molecular mechanisms of MafB regulation of epidermal development, we performed microarray analysis of mRNAs isolated from dorsal skin epidermis of MafB-/- and wild-type mice at E18.5. Epidermis was separated from dorsal skin tissues of E18.5 mouse embryos (MafB-/- and WT) by Dispase (Life Technologies) treatment. Total RNA was isolated using Trizol reagent (Life Technologies), purified using an RNeasy mini kit (Qiagen), and subjected to microarray analysis.