Laser Capture Microdissection RNA-seq in Pocillopora acuta
Chapter two of my dissertation, now published in PLOS One (2026).
We used Laser Capture Microdissection to isolate distinct tissue regions of the reef-building coral Pocillopora acuta, then performed RNA-seq to identify location-specific gene expression.
Publication
Dellaert, Z. and Putnam, H. M. (2026). Spatially resolved gene expression analysis illuminates location-specific functions in the reef-building coral Pocillopora acuta. PLOS One 21, e0358454. Open Access!
Data and code
All analysis code is on GitHub. Raw sequencing data is available on SRA under BioProject PRJNA1209584.
Key analysis pipelines:
- Bioinformatics pipeline (raw reads to gene counts)
- Differential expression (DESeq2)
- GO enrichment with Viseago/topGO
- Code for plotting the published figures
- Supplementary tables
Expression in the dissected tissues was compared to the published coral “biomineralization toolkit” (Scucchia et al., 2021a; 2021b) and the Stylophora pistillata single-cell atlas (Levy et al., 2021).