Genome-wide transcriptomic analysis in pediatric glioblastomas cell lines by RNA-seq.

We identified that RACK7 recognizes the histone H3.3G34R mutaion in vitro and in vivo. In order to explore the function of RACK7 and H3.3G34R mutaion, we used three pediatric glioblastomas(pGBM) cell lines. SJ-HGGx6c(R6) and SJ-HGGx42c(R42) have heterozygous G34R mutation, while SJ-HGGx39c(WT39) has wildtype H3F3A, which encodes H3.3. We next corrected H3.3G34R in R6 and R42 cells to wildtype H3.3 by CRISPR/Cas9 mediated knock-in, and knocked out RACK7 in R6 and R42 cells by CRISPR/Cas9. Finaly, we performed genome-wide transcriptomic analysis in these cell lines by RNA-seq analysis. Overall design: The mRNA was captured and deep sequenced in the pGBM cell lines on Illumina Hiseq X-Ten with 2×150 bp paired-end sequencing, two biological repeats for each cell lines were used.