Formaldehyde fixation and RNA Seq - possible?

[Dolphin22]

Hey there

We have done Helicos Sequencing of Arabaidopsis RNA. The tissues were crosslinked with formaldehyde and the FA was washed away before putting into the sequencer. Analysis revealed that we had only low percentages of aligned reads.
I would suspect that this comes from the FA treatment. What do you think? Might another sequencing technology solve this problem or is generally difficult to sequence FA treated samples?

Thank you for your opinions.

[yvan.wenger]

Hi,

Did you find out what was happening? Was the low alignment rate indeed due to the FA treatment ?

Best,

Yvan