Hi,
I am new to the field of RNA sequencing. I want to know which is the best way to analyse RNA sequencing data from illumina without replications. I describe briefly my experiment and would be grateful if some one could suggest me ways to analyse the data.
I work on forest trees and they are outbreeding like humans. I have used 3 populations with 15 seedlings from each population. I have grown 15 seedlings from each population in a glasshouse for 4 months and then imposed water stress by giving them limited amount of water for 2 months. I have taken leaf samples for RNA just before imposing stress. Ten seedlings recieved stress treatment and the other five were well watered. I have taken leaf samples one month and two months after treatment. I have bulked the RNA from initial sampling from 10 seedlings which recieved stress treatment and bulked the RNA from the other five seedlings. I did the same with the stress treated seedlins and sequenced all five bulks (3 bulks from stressed including one before imposing stress and two from controls C0). Five RNA bulks were sequenced using Illumina.
Is it valid to compare expression from the ten seedlings before and after stress treatment? I don't have any replications. Could I use DEseq for analysing this data as I don't have replications?
I am new to the field of RNA sequencing. I want to know which is the best way to analyse RNA sequencing data from illumina without replications. I describe briefly my experiment and would be grateful if some one could suggest me ways to analyse the data.
I work on forest trees and they are outbreeding like humans. I have used 3 populations with 15 seedlings from each population. I have grown 15 seedlings from each population in a glasshouse for 4 months and then imposed water stress by giving them limited amount of water for 2 months. I have taken leaf samples for RNA just before imposing stress. Ten seedlings recieved stress treatment and the other five were well watered. I have taken leaf samples one month and two months after treatment. I have bulked the RNA from initial sampling from 10 seedlings which recieved stress treatment and bulked the RNA from the other five seedlings. I did the same with the stress treated seedlins and sequenced all five bulks (3 bulks from stressed including one before imposing stress and two from controls C0). Five RNA bulks were sequenced using Illumina.
Is it valid to compare expression from the ten seedlings before and after stress treatment? I don't have any replications. Could I use DEseq for analysing this data as I don't have replications?
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