Second Year Talks: Stylasterid Corals: Insights into palaeoceanography and biomineralisation and Using computational method to determine the phylogenetic of single-cell data
James Kershaw, University of Bristol and Tianqi Shi, University of Bristol
James Kershaw (University of Bristol): Stylasterid Corals: Insights into palaeoceanography and biomineralisation
Stylasterids are an abundant group of deep-sea coral (DSC). Despite their widespread distribution and hard, carbonate skeletons implying high potential as a palaeoceanographic archive, studies of inorganic Stylasterid geochemistry remain scarce. We show that metal/Ca ratios and the boron isotope signature (δ11B) of Stylasterid skeletons are controlled by key ocean properties and processes including temperature, pH, primary productivity and circulation geometry. Additionally, we present the first attempt to apply U-series dating techniques to Stylasterid skeletons. Their unique skeletal geochemistry apparently results from a greater degree of equilibrium with seawater compared to other DSC groups, providing important insight into coral biomineralisation.
Tianqi Shi (University of Bristol): Using computational method to determine the phylogenetic of single-cell data
The analyze of single-cell sequence has been one of the most important method in biostatic right now and the reading and analyzing of single-cell data was valuable for us to dig in. Currently we were trying to analyze the Mus musculus retina RNA-Seq Drop-seq with public methods, which will help us to understand the single-cell data specially the RNA-Seq. The data we chosen was the data from Macosko 2015. And currently we only looking into the replicate 1 of the drop-seq analysis of p14 retina. Which contain around 15000 cells. We start to run the data we have base on an online open-source python script to help me understand the output, the script was post on google colab and was easy use to create knee-plot or T-SNE plot. Also, with some modify on the code, it was easily to create the files that will link each barcode to the cluster we notice, and those can be used to identify the annotate cluster plot and mark the cluster with cell group. These cell group will be used in the future analyze in phylogenetic tree.
For the tree we got, we use the p14 retina merged digital expression file post by Macosko, we change the format of the matrix to a 0/1 matrix and which means all the gene that express in the cell type will be marked as 1 and the rest should be 0. Then with the data we create we can use iqtree to create the phylogenetic tree. It takes some time to choose the modules we use but once we chose the module, we can have the tree.
When we combine the tree with the cluster-barcode file, we should be able to have the annotate cell tree. If all the analyze goes right, we should be able to have a tree which has all the cluster separately and that result will have a positive result to the next of my study
Talks will be held on Zoom using this link: https://zoom.us/j/96309344441.