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Joseph Cardiello
Year 1 blog update
Year 1: October 1, 2018-September 1, 2019
Sie Foundation Fellowship

The first year of being funded by the Sie Foundation Postdoctoral Fellowship has been quite eventful as I set out to learn a host of new wet lab techniques, analysis methods, and a new biological perturbation to wrap my head around: trisomy 21. My favorite current project focuses on whether cells with three copies of chromosome 21 display more RNA level variations than cells with two copies. We hypothesized that having a third chromosome 21 may complicate the ability of cells to evenly express RNA levels across a cell population. I began testing this hypothesis by generating single cell RNA-seq data for paired cell lines, derived from white blood cells of two brothers: one who is trisomic for chromosome 21 and another who is not. The data for this project is relatively new and I am still consulting with various researchers about how best to statistically test these hypotheses. So far it appears that cells with trisomy 21 may display increased variability in some RNA levels, but these results are preliminary and still need to be robustly tested statistically and followed up with more experiments.

Each of my initial projects have required the use of large data processing pipelines, bioinformatic analyses and custom data analysis, all skills that I’ve been working towards acquiring in the Dowell Allen lab. To this end, upon joining the Dowell Allen lab I learned to process data on the BioFrontiers Fiji distributed computer. I also learned to use faster data processing pipelines developed by members of the Dowell Allen lab. Finally, I began learning to do some of my own coding and analysis using the python coding language. The learning curve for this analysis has been steep, but it’s been a welcome challenge as the ability to write custom code is hugely rewarding in opening up the number of scientific questions I can ask of my data.

I’ve also taken this year to learn more about science education and to work on my writing skills. This summer I took an introduction to evidence-based teaching course offered at CU Boulder and attended by postdocs from around the country. The course introduced a wide variety of active learning methods that I hope to apply to future teaching experiences. I also taught one day of the short-read workshop class that the Dowell Allen lab holds each year to give researchers an introduction to sequencing analysis. It was an exciting challenge to make this tutorial on the analysis of ChIP-seq and ATAC-seq, two next generation sequencing methods, interactive and accessible to the wide range of students in the course. I also mentored a graduate student in the lab, and she subsequently joined our lab. Finally, as a team, with Robin Dowell, Mary Allen, and another postdoc in our lab, Gilson Sanchez, I helped write a review paper on enhancer RNAs. This has been a great first year on this fellowship and I can’t wait to see what exciting results my projects produce over the next year.