SEQ experiment w. Human ESc as reference

[Agun]

Dear all.

We are doing a RNA sequencing project in which we want to compare RNA sequencing profiles to each other and to human embryonic stem cells as a reference. The aim is to find differently expressed genes between my cells.

Since many persons already have sequenced hES cells, do I really need to buy a hES line and sequence it just to get the same results as all other have gotten?

One could think that I just need to sequence my stem cell populations and afterwards compare differently expressed genes to hES profiles that already have been sequenced?

Thank you for answer.

King regards,

Anders

[dpryan]

It's just a question of how much of a batch effect is present. If you culture the ES cells yourself and perform extraction/library prep with your other samples then you needn't concern yourself with that issue.

[Agun]

If I need to sequence the hES myself, then I'll have to send the RNA for library prep at the same time as the other samples. (Hiring a company to make the prep)

One could save triplicate library preparation and sequencing cost to out on other samples if there is acceptable to use already generate data for hES. Since there is only a few cell lines to buy, all of them should be showing the same anyway if cultured correctly.

So the question is more, is it acceptable to compare my data to hES RNA-seq data that somebody else have made to find differently expressed stem cell relevant genes or do I actually need to perform the RNA-seq myself?