Protrusion vs cell-body mRNA analysis by RNA-seq

We quantified the distribution of cellular mRNAs between protrusions and cell-body of MDA-MB-231 breast carcinoma cells by RNA-seq, using a filter based fractionation method. In this method, cells are seeded on top of 3micrometer transwell filters to enable protrusions to form but to prevent the cell-bodies passing through due to the small size of the pores, thus resulting in separation of protrusions and cell-bodies on opposite sides of the filter, from which RNA can be prepared separately. RNA samples for Illumina sequencing were generated in duplicates from two biological replicate experiments (two protrusions and two cell-body).