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I need to understand the level of RNA over-expression that is normally reached with HEK293 T-REx Flp-In cells. This over-expression system is widely used in PAR-CLIP experiments, which is why I want to understand it. I asked some gene-expression experts, but so far nobody give an estimate. Here I would like to ask for a reputable source, while "gut-feeling" estimated would be helpful as well.

Additionally, to give an idea how I tried to approach this question, here I found a data-series that could finally reveal the answer:

https://www.ncbi.nlm.nih.gov/gds/?term=GSE44616%5BAccession%5D

Expression of FLAG/HA-LIN28A or FLAG/HA-LIN28B was induced by addition of 250 ng/ml doxycycline 15 to 20 h before crosslinking.

This contains 2 replicates of RNA-seq with and without induction of LIN28A or LIN28B. So the idea is to ascertain the expression level of LIN28A/B with or without induction, relative to the whole transcriptome. However, the file uses read identifiers like "213084_x_at" instead of transcript/gene names/IDs, and I don't know how to map them to genes automatically.

Similar to this idea, has anyone maybe read any other papers where HEK293 T-REx Flp-In overexpression is performed, that measure the RNA levels?

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  • $\begingroup$ This is going to depend a lot on your cells - age, passage number, origin, confluence, growth conditions, media used, how stressed their predecessors may have gotten at some point(s), possible contamination with other cell lines, etc. There is no one "true" reference HEK293 cell line anymore (as far as I'm aware), as they've been used and shared all over the world. The 293s that I have in liquid nitrogen in my lab and the ones you have in yours could be very different from each other. $\endgroup$ – MattDMo Jan 11 at 15:28

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