ATAC-seq data in MEF and mESC sequenced by BGI DNBSEQ-G400 platform and Illumina HiseqX10 instruments

We benchmark Illumina's HiseqX10 instrument against Beijing Genomics Institute's (BGI) DNBSEQ-G400 platform, a considerably cheaper sequencing alternative. For comparisons, the same bulk ATAC-seq libraries generated from pluripotent stem cells (PSCs) and fibroblasts were sequenced on both platforms. Both instruments generate sequencing reads with comparable mapping rates and genomic context. However DNBSEQ-G400 data contained a significantly higher number of small, sub-nucleosomal reads (>30% increase) and a reduced number of bi-nucleosomal reads (>75% decrease), which resulted in narrower peak-bases and improved peak calling, enabling the identification of 4% more differentially accessible regions between PSCs and fibroblasts. Ability to identify master TFs that underpin the PSC state relative to fibroblasts, including aggregate and de novo foot-printing capacity, were highly similar between data generated on both platforms. Overall design: Comparative open-chromatin profile (ATAC-seq) for PSCs and fibroblasts. OMNI-ATACseq libraries were generated from FACS purified cells (in case of MEFs: Thy1+ ; in case of mESCs: Thy1-/Ssea1+/Epcam+) according to the standard protocol (see doi: 10.1038/nmeth.4396). Afterwards, libraries were purified using a QIAGEN MinElute PCR purification kit (QIAGEN, Cat#28004) followed by Agencourt AMPure XP beads (Beckman Coulter, Cat#A63880) according to the manufacturer's recommendations. Library fragments ranging from 150 to 700 bp were enriched and the final elution volume was 21 ul. The finalized libraries were provided to BGI for sequencing. HiSeqX10 sequencing was performed in 150bp PE mode followed by read trimming to 100bp PE for analysis. In case of sequencing on the DNBSEQ-G400 instrument libraries were converted to nanoballs and sequenced according to established workflows in 100bp PE mode (see doi: 10.1093/nargab/lqaa034).