SLIC-CAGE of paired-end sequencing data in mouse islets

Super-Low Input Carrier Cap Analysis of Gene Expression (SLIC-CAGE) to identify transcription start sites (TSS) and existing genome-wide maps of islet histone marks to characterise the contribution of transcriptional regulation of LKB1-mediated control of gene expression in mouse ß-cells. SLIC-CAGE was performed as in (Cvetesic et al. - doi: 10.1101/gr.235937.118) using 100 ng of total RNA extracted as described above from islets isolated from a 18 week old female mouse on a C57BL6/J background. 12 cycles were performed for library amplification. The amplified library was purified with AMPure XP beads and visualised using a HS DNA chip (Bioanalyzer, Agilent). The library was sequenced on a HiSeq2500 instrument with paired-end, 150bp reads). SLIC-CAGE paired-end sequencing data was aligned to GENCODE assembly annotation version GRCm38.p6 using the STAR alignment tool v2.4.2a.