ATACseq of differentiating ATDC5 mouse prechondrocytes

We report the application of ATACseq to differentiating ATDC5 cells with the aim of identifying how chromatin architecture is changing as these cells move from pre-chondrocytes to differentiated chondrocytes. Raw data was generated by sequencing using the Novaseq6000 with 50bp single end reads. Trimming to remove adapters or poor-quality reads was performed with no sequence below 30 nucleotides in length used in the analysis. We found that there were significant changes in chromatin accessibility at both days 3 and 10 of differentiation. Using diffBind, differential peaks were identified at day 3 and 10. These peaks were further analyzed for enriched transcription factor binding sites and identified motifs for the RUNX family transcription factors as well as SOX9. Overall design: ATACseq of ATDC5 cells at 3 time points of differentiation.