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Old 04-10-2014, 05:28 AM   #3
dodo1981
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Location: Australia

Join Date: Apr 2014
Posts: 4
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Hi Alejandro!
Thank you for the quick answer. I would be very happy if you could help me and give me some good feedback.

Now the answers:
1) First step of my Phd was to find (and annotate) 12 proteins of interest in 9 species of amoebas. I have RNA-Seq data for 2 of these 9 amoebas (own experiments). For these two amoeba species I have already assembled their transcriptomes (de novo using Trinity). Material for sequencing was collected in the same growth stage. For remaining 7, I don't know the exact sampling conditions, but the data (transcriptomes and genomes) are available in Genbank, so maybe information is there. One problem: there is no genome sequence for one of our two amoebas.
About replicates: I have two replicates (two rounds of sequencing) for one of the amoebas. They are from the same total RNA but sequenced by two different platforms: HiSeq and GA2.

2) I am interested in analyzing gene expression of the 12 proteins in all 9 species of Amoeba. Yes, differences in expression between the amoebas. As I wrote above: the genomes are available, with exception of one of the sequenced amoebas for which I have assembled transcriptome.

Thank you Alejandro and I am looking forwar to see your answer

Dorota
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