PCR Results Gel, take 3

This gel shows the results of the last PCR run, contrasted against a new one from this afternoon. In both cases, the amount of product that was run was decreased from 5 to 2 ul. Unfortunately, there is still a visible band in the negative control position. Also, band six does not show great amplification. However, it also does not show the excess primers that the negative controls demonstrate. It could be possible that either something was off when the PCR reaction was set, such as fewer primers, or I made a mistake when loading the gel, and somehow got less product from this sample into the well.

Batch analysis of sequence data

So Reid and I think we've found a good way to batch-analyze all the sequence data we'll be getting back from WashU.

Steps:
1) Convert chromatogram reads to sequence files in FASTA format:
We may not have to worry about this step, as we can probably just ask WashU to send us FASTA files for our sequences. Currently, to do it ourselves, we have to open each file individually with FinchTV and use File-->Export-->DNA Sequence:FASTA.

2) Convert individual FASTA-formatted sequence files to one large Multi-FASTA file containing all the sequences:
FASTA sequence is just a way formatting a plaintext file so that it can be understood by databases such as NCBI. For each entry, the first line contains a ">" symbol followed by the name you want to give that sequence (no space between ">" and the name). The sequence is on the next line. (FASTA can be used for both nucleotide and amino acid sequences; for more info, visit wikipedia: http://en.wikipedia.org/wiki/Fasta_format)
I found a freeware tool that can take a folder full of FASTA sequence files and process it into a Multi-FASTA file. It is available here: http://3d2f.com/download/48-830-fasta-converter-free-download.shtml.Click on the link I've indicated in the screenshot to download.
To use the program, select a folder the folder containing the sequence files you want to merge, and click Start. Make sure you have selected "All files" in the drop-down menu; otherwise, the program only looks for .fasta files and not other sequence files. The program automatically puts the merged file in the same folder as the individual files.

3) Analyze and classify using greengenes:
Greengenes (http://greengenes.lbl.gov/cgi-bin/nph-index.cgi)is a tool for batch analysis of 16S rDNA sequences--exactly what we need to do! It analyzes and prunes your input sequences (in multi-FASTA format) to things that it agrees are 16S genes. It then compares those sequences to several databases of 16S rDNAs and produces a nifty spreadsheet telling you what group (often genus; species if you're lucky) each sequence belongs to.
To align your multi-FASTA sequences, go to the align icon at the top of the greengenes homepage. Upload your file, enter your email address, and hit "Process Fasta File". We are still working on figuring out what all the parameters on the page do, but adjusting "Significant Match Requirements" to minimum length of 250 or 300 allows it to process more of our files--it throws out any that are shorter than that.
Within a few minutes the program will send you an email with the subject line "Greengenes: Your NAST-aligned sequences". You will need Stuffit Expander to open the attached .tgz file. If you didn't change anything under "Files you desire" when doing the alignment, this file will contain a file with all your NAST-aligned sequences in FASTA format (lots of dots and dashes), as well as a spreadsheet summarizing what sequences the program kept and which it threw out (eg, for being too short).
Now return to Greengenes and go to the "Compare" icon at the top of the page. Click on "classify" (third bullet point) Upload your NAST-aligned FASTA file, enter your email address, and click "Classify Batch".
You will receive an email with the subject "greengenes classification results" and an excel file attached that classifies all your sequences!


The End.

I hope this post wasn't too long/boring/unnecessarily detailed.
Please feel free to add anything I forgot or any tips you may come across as we start getting sequences back in a few weeks!
~Frances

colony PCR info

Reid and I just talked to Liz about doing colony PCR on the bacteria currently growing on our plates. We found a protocol (http://www.cbs.umn.edu/labs/perry/Protocols/bactPCR.html) that Liz thought would work--basically you suspend a colony in lysis buffer, heat it for a while, spin it down, and use the supernatant as your PCR template.

Since lysis is more reliable on cells that haven't reached stationary phase, we will probably want to have fresh overnight colonies to use for this--instead of liquid cultures, we'll just grow them on agar.

We have also asked Liz to order more of those pre-mixed PCR kits for us. I don't think we/Amy's lab have enough tubes left to do all the colonies we talked about doing (~3 of each type from each anemone line), so we might have to wait to pick colonies until we know that the new PCR kit is on the way.

~Frances