GSE175403
Alternative splicing changes are associated with pre-birth adaptation during mouse lung development
Analysis of gene expression and alternative splicing changes in mouse lungs at different developmental time-points (E15.5, E18.5, P5, P8) was performed through RNAseq. We performed 101 nt paired-end RNAseq using HiSeq 4000 on triplicate samples. We obtained an average of 59.8 million reads per sample.   The sequence reads that passed quality filters were analyzed at the transcript and at the alternative splicing events level using using D  For gene expression analysis, the ~56.8 M raw reads generated per sample were uniquely mapped to the mm10 assembly and annotated to the Gencode vM14 transcriptome using TopHat2, with Bowtie2. Gene expression levels were quantified with HTSeq-count (version 0.10.0). After applying quality filters, we obtained 16,152 expressed genes for downstream analysis.   For AS event-level analysis, raw reads were mapped to previously annotated AS events for the mouse reference assembly (mm10 vastdb.mm2.23.06.20) from VastDB (VastDB v2 released). Abundance of AS events in Percent spliced in (PSI) values was estimated using VAST-TOOLS.  We found that most of the AS changes during alveologenesis occur at the perinatal period in genes associated with blood vessel and epithelial cell development. In particular, we found that Vegfa undergoes AS in lungs at the transition from embryonic to post-natal life, starting at the end of the embryonic period. Our results suggest provide a framework for understanding how AS changes impact on lung development during the critical period of transition to the postnatal life. Overall design: RNAseq data sets of bulk mouse lung tissue collected at E15.5, E18.5, P5 and P8. Samples were collected in triplicates.