Week 6 : Adil

This week I continued working with the ICSBCS sequencing datasets. We also got access to the docker image of the deconvolution package we plan to use for immune cell fraction analysis. We still have few WGS and RNAseq datasets to analyze. We shortlisted a few samples which have both WGS and RNA datasets for own downstream analyses. We are also interested to integrate H&E stained image data in our data analysis. So I spent sometime with Dr. Newman's group members trying to identify the samples which already have H&E data and samples for which we need to capture the H&E images. On the experimental front we are trying to collect more samples to run trovo experiments wherein we capture, isolate and culture T cells and tumor cells. We then run sequencing experiments to understand T cell activity in these samples (the TCR seq library we submitted for sequencing a few days back is also a part of this analysis). Overall it was a heavy week in the lab!