Bulk_RNA_seq_of_epithelioid_punch_biopsy
We are studying the mechanism of mutant clone expansion using epithelioid culture made from mouse esophagus. The idea is to isolate epithelioid cells at different location of a mutant clone using small punch biopsy. RNA will be extracted from these cells and sequenced to compare the transcriptomics. This will provide us a clue, for example, what genes/pathways are differently expressed in cells locating to the center vs edge of a mutant clone. The challenge of the study is that the punch biopsies will be very small (0.25mm diameter) to isolate low number of cells (<100) at different locations of a already small mutant clone. So, we will test how well it works on wild type cells before moving on to mutant clones.
This study is to apply low input RNA sequencing pipeline on RNA extracted from small punch biopsies of epithelioid culture to study the mechanism of mutant clone expansion.