ATAC-seq Analysis of Cryopreserved Jejunum

The cryopreserved jejunum was sent to Active Motif for ATAC-seq experiments. The nuclei isolated from the tissue were tagmented (fragmented and tagged with sequencing adaptors) by hyperactive Tn5 transposase as described previously^{72 (link)} with some modifications^{73 (link)} using the reagents in Nextera Library Prep Kit (Illumina). After amplification with ten cycles of PCR, the resultant DNA was sequenced with PE42 sequencing on the NextSeq 500 sequencer (Illumin). Sequence reads were aligned using the BWA algorithm,^{74 (link)} and peaks in the histograms were identified using the MACS 2.1.0 algorithm at a cutoff of p value 1 × 10⁷. Signal maps and peak locations were analyzed using Active Motifs proprietary analysis program, and reads counted in all merged peak regions were compared using DeSeq2.^{75 (link)}