GSE131919
Transcriptome profiling of Embryonic day 9.5 WT and Clpex mutant mice
Purpose: To determine the differentially expressed genes in the whole E9.5 Clpex mutant embryo, a hypomorph of Pgap2 of the glycosylphosphatidylinositol biosynthetic pathway. Overall design: 5 WT and 5 Clpex mutant E9.5 embryos were snap frozen on dry ice. RNA was isolated and pooled samples of each genotype were used for paired-end bulk-RNA sequencing (BGI-Americas, Cambridge, MA). RNA-Seq analysis pipeline steps were performed using CSBB [Computational Suite for Bioinformaticians and Biologists: https://github.com/csbbcompbio/CSBB-v3.0]. CSBB   has multiple modules, RNA-Seq module is focused on carrying out analysis steps on sequencing data, which comprises of quality check, alignment, quantification and generating mapped read visualization files. Quality check of the sequencing reads was performed using FASTQC  (http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc). RNA-Seq reads for the mutant and wildtype were paired-end and had ~43 and ~31 million reads respectively.Differential expression analysis was carried out by EBSeq [https://www.biostat.wisc.edu/~kendzior/EBSEQ/]. Differential transcripts are filtered based on LogFC and p-value. Filtered DE transcripts are used for functional and pathway enrichment using toppgene [https://toppgene.cchmc.org/]