NextSeq 500 sequencing; QUANTSEQ 3' sequencing of protrusions and cell bodies of control (NT) or LARP6 siRNA (LARP6 KD) transfected MDA-MB231 breast cancer cells
QUANTSEQ 3' sequencing of protrusions and cell bodies of control (NT) or LARP6 siRNA (LARP6 KD) transfected MDA-MB231 breast cancer cells
Samples were collected by lysis of protrusion and cell-bodies from opposite sides of the transwell filters. Lysis was done in QIAGEN RNAeasy RLT buffer. Cells were transfected with control or LARP6 siRNAs for 48hrs before being seeded on 75mm Collagen-I coated transwell filters (3 micron pore size). Cells were allowed to adhere overnight without any media added to the bottom of the filter Next day, protrusions were induced by addition of media to the bottom chamber. Media on the top was also changed at the same time. Cells were allowed to form protrusions for 2 hrs. RNA was purified using QIAGEN RNAeasy extraction kit according to manufacturer's instructions Library prep was done using Lexogen QUANTSEQ FWD 3'mRNA sequencing
Experimental Factor: RNA interference
scrambled siRNA
Experimental Factor: fraction
cell body