Hi all. This is a shot in the dark, but I was wondering if anybody could help me understand broadly how preparing a sample for sequencing works, like everything that happens from petri-dish (or cheek-swab, fecal sample, etc...) to the point that it goes into the machine. I have frankly a million questions for anyone who can help. In fact, if anybody is willing to spend 30-45 minutes talking me through some of these by phone/skype, I could buy you something nice from your Amazon wishlist, for example.
For example, let's say I want to sequence the genome of Salmonella, serotype XYZ. I'm assuming that first I have to get my hands on a sample of that, but then what? Does it need to be cultured to a certain critical mass? Do I need to test that I've got the right serotype first? And once we have a reliable sample, what do we do then?
I've seen references to "purification" happening at this stage; what is involved in that? I've also read references to samples having to be so many ng/uL (I think those units are right...), so is the rest just water, or is it a specific solution?
And as for a specific example, I was looking at the JGI database for a species of algae, and someone had sequenced the DNA, and separately also the Transcriptome (ESTs) with 454 and just posted the raw SSF files. I want to ask for more information about what that contains but I don't know where to start and what a biologist who has used 454 (which is not me) should already know.
I know that's a lot of questions and obviously I have a lot to learn, but of course anything would be helpful, or even any resources to read. And if you want to let me ask you questions over the phone in exchange for a gift, send me an email through the board :-) Thanks in advance.
For example, let's say I want to sequence the genome of Salmonella, serotype XYZ. I'm assuming that first I have to get my hands on a sample of that, but then what? Does it need to be cultured to a certain critical mass? Do I need to test that I've got the right serotype first? And once we have a reliable sample, what do we do then?
I've seen references to "purification" happening at this stage; what is involved in that? I've also read references to samples having to be so many ng/uL (I think those units are right...), so is the rest just water, or is it a specific solution?
And as for a specific example, I was looking at the JGI database for a species of algae, and someone had sequenced the DNA, and separately also the Transcriptome (ESTs) with 454 and just posted the raw SSF files. I want to ask for more information about what that contains but I don't know where to start and what a biologist who has used 454 (which is not me) should already know.
I know that's a lot of questions and obviously I have a lot to learn, but of course anything would be helpful, or even any resources to read. And if you want to let me ask you questions over the phone in exchange for a gift, send me an email through the board :-) Thanks in advance.
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