GSE112714
Analysis of MGE Transcriptomes with or without Ctnnb1 knockout in human through RNA Sequencing
Purpose: Understand the cues that orchestrate the expansion or differentiation of medial ganglionic eminence (MGE) progenitors no matter in vivo or in vitro. Methods: Total RNA from each sample was used to prepare the library. Then the libraries were sequenced at 50bp single read on an Illumina HiSeq 2500 platform. Sequencing reads from each sample were mapped to the human reference genomes (hg38 version) by using TopHat v2.1.1. The mapped reads were further analyzed by cufflinks v1.3.0 and the expression levels for each transcript were quantified as Fragments Per Kilobase of transcript per Million mapped reads (FPKM). For differential expression analysis, sequencing counts at the gene level were obtained using HTSeq v 0.9.1. R package DESeq2 was then used to identify differential expressed genes between different conditions.Statistically enriched functional categories of genes were identified using DAVID 6.8. PPI networks were constructed by using STRING v10.0 . Results: Transcriptome profiling reveals that ablation of ß-catenin in MGE cells leads to advanced neuronal differentiation, while activation of Wnt/ß-catenin signaling keeps the MGE cells in an undifferentiated progenitor state. Conclusions: Wnt signaling is a key player in governing self-renewal vs terminal differentiation of MGE progenitors both in vivo and in vitro. Overall design: mRNA profiles of MGE cells with or without Ctnnb1 knockout were generated by RNA sequencing, using Illumina Hiseq 2500 platform.