ORCID Identifier(s)


Document Type

Honors Thesis


Assay for transposase accessible chromatin with high-throughput sequencing (ATAC-seq) is a method used to study the accessibility of chromatin in a eukaryotic DNA. In eukaryotes, the DNA is packaged into chromatin to fit in the nucleus. The accessibility of chromatin by the proteins is determined by its packing status. In this research, an adapted protocol of nucleic ATAC-seq was performed on Daphnia pulex, a planktonic crustacean, to optimize it and generate a chromatin map. ATAC-seq was performed on 150 and 500 Daphnia pulex, following three major steps: nucleic isolation and purification, transposition reaction, and polymerase chain reaction (PCR) library amplification. The TapeStation analysis results indicated that the optimum input for ATAC-seq of Daphnia pulex was 500 animals. The modification of the protocol will be useful for future investigation in not only the whole body but tissue-specific studies.

Publication Date




Faculty Mentor of Honors Project

Sen Xu



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