GSM3262255: control_136176; Xenopus laevis; RNA-Seq
facial region (area between the eyes from the midface to the cement gland, without eyes or brain tissue) was manually dissected from 500 embryos. Dissected regions were pooled and total RNA extracted with TriReagent following standard protocols RNAseq was performed by Hudson Alpha Institute for Biotechnology (Huntsville, AL) where a HiSeq v4 PE100 250 mil reads 50 GB max output with Teir 1 analysis performed.   Reads were aligned using Xenopus laevis reference genome and STAR alignment software, and then counted using featureCounts software in the Subread package (http://www.xenbase.org/, RRID:SCR_003280) [29-31] The DESeq2 Bioconductor package in the R statistical computing environment to normalize count data, estimate dispersion, and fit a negative binomial model for each gene [32-34]. R Code available upon request. Data was then exported to Excel for further analysis. Xenopus genes that were significantly altered (p<0.05) were converted to the human ortholog for functional and network analyses (93 unique genes). Genetic similarity was determined to be >90% identity and similarity.
GEO Accession
GSM3262255