newbie- need some good background

[kaikat]

Now that I've gotten my microarrays to look consistently gorgeous, we've decided to start sequencing...
I'm somewhat used to baptisms by fire, but I'm having problems even GOOGLING what I'm supposed to be doing. The illumina TruSeq manual isn't helping, either.
Any of you experienced folks have any suggestions/sources for good background on my new adventure??

[GW_OK]

I've found the Truseq manual to be pretty straight forward as protocols go, actually. Perhaps you should elaborate more on what's giving you trouble. Have you read much of the rest of the forum?

[kaikat]

Just found the forum today, and am switching back and forth browsing the forum, editing a paper, entering data, juggling students and dealing with HR...
To be more specific... I have NO CLUE where to start. I've got RNA, need to sequence their transcriptome. Can generate cDNA, label and hybe like a madwoman on a mission. I know the gist of AFLP sequencing, used to do MAS for soybeans... microarray data and analysis, no problem. Was told sequencing using TruSeq kit was the way to go. Said "sure, we can do that," and then found out I'm the guinea pig of the group.
I'm not having trouble yet, but this isn't my first dog and pony show... murphy's law loves me... cliche, cliche, cliche

I think I'm just missing a BASIC page or two of what I need to know... looking for any basic primer.

Thanks!

[GW_OK]

I take it you're not the one running the sequencer? If you're just making libraries to send off to someone, well, the protocols are pretty easy to follow. If you're wanting to know how to analyze your RNA-seq data I would continue to have a look around the forums, particularly bioinformatics.

[kaikat]

yes, we're sending them off. We're working with a physiologist who's going to analyze the data.

[GW_OK]

Sounds like you're good to go then. Make your libraries, send them off, hand the data that comes back to the physiologist, get his analysis back and write a paper. That's about as nice a setup as you can get.