We want to investigate the endogenous LINE1 expression levels in different cells. To do this, we will use a RNA-seq strategy after a-ORF1 affinity capture in different cell lines, among which different potent states of PA-1 cells (see Maria Benitez' Journal).
In addition, we will do protein analysis on these samples to investigate how expression levels relate to the protein levels in the same samples.
We will use the following cells:
1) PA-1 (PC)
2) PA-1 (DC)
3) N2102Ep
4) NTERA2As of august 2020, RNA seq has been performed at NYU and analyses are currently underway.
Hua ran the saved protein fractions on a gel and did western blots on all fractions –> June 16, 2020 - Western Blots of Lars' samples
Hua did some testers on the recovery of the organic phase from the phasemaker tubes. These resulted in a final protocol (July 21, 2020 - AmAc/MeOH precipitation of protein from anti-ORF1 elution in organic phase) in which organic phase from the phasemaker tubes was captured, proteins precipitated, prepped for MS and sent to ERIBA. Luciano is currently working on these samples.