Key Features
Enhance your research with our curated data sets and powerful platform features. Pluto Bio makes it simple to find and use the data you need.
Learn MorePurpose: This study aims to identify the differentially expressed genes in adult left ventricles treated with caffeine during early embryogenesis. Methods: Pregnant CD-1 mice were treated with vehicle (normal saline) or 20 mg/kg caffeine via i.p. injection once daily during embryonic day (E) 6.5-9.5. Pups were born and raised to one year of age. Left ventricles from adult male mice were dissected and used for total RNA isolation with the RNeasy Plus Mini kit (Valencia, CA, USA). mRNA was isolated from total RNA using NEXTflex Poly(A) Beads (Bioo Scientific, Austin, TX, USA). Sequencing libraries were prepared with the NEBNext mRNA Library Prep Master Mix Set for Illumina (NEB, Ipswich, MA, USA) and the NEBNext Multiplex Oligos for Illumina (NEB). Illumina-adapted libraries (n=3/treatment) were pooled at equal molar ratio and sequenced with one High Output 1x75 cycles run on a NextSeq500 sequencer (Illumina, San Diego, CA, USA). The fastq files generated from RNA-Seq were uploaded to the UF Research Computing Galaxy instance developed by the University of Florida. The data were cleaned with the following steps: removed sequencing artifacts, trimmed 5 or 3 ends with low scores, removed adaptor contamination, and filtered low quality reads by the FastQC program. The remaining high quality RNA-Seq reads were mapped to the mouse genome (mm10) with the Tophat2 tool. Counting of RNA-Seq reads were performed with HTSeq. Differential expression (DE) of genes between treatments was analyzed using R package EdgeR, with Ensembl Mus_GRCm38.79.gtf as the reference annotation. Genes with false discovery rate (FDR) less than 0.05 and absolute fold change greater than 1.5 were considered as significant. Results: DE analysis revealed that 85 genes were up-regulated, and 31 genes were down-regulated in the adult left ventricles treated with in utero caffeine. SOURCE: Xiefan Fang (xiefanfang@ufl.edu) - University of Florida
View on GEOView in PlutoEnhance your research with our curated data sets and powerful platform features. Pluto Bio makes it simple to find and use the data you need.
Learn MoreUse Pluto's intuitive interface to analyze and visualize data for this experiment. Pluto's platform is equipped with an API & SDKs, making it easy to integrate into your internal bioinformatics processes.
Read about post-pipeline analysisView quality control data and experiment metadata for this experiment.
Request imports from GEO or TCGA directly within Pluto Bio.
Chat with our Scientific Insights team