Resources for drought genes in sunflower

Recently, I hassled people until they gave me places to look for lists of genes expressed in response to drought treatment in Helianthus. Perhaps you will find it useful too?

Marchand et al. 2014 drought gene regulatory network:

Based on experimental data from Rengel et al. 2012:

And more in Marchand’s thesis:

Additionally, Min has some data/preliminary analysis from a microarray study in sunflower. Contact him for more info?

Silica gel: God’s gift to botanists

Another Rieseberg lab member was asking me this week about preserving plant tissues on silica gel for later DNA extraction, and this got me to thinking about the general idea. I thought I would make a post about it, since it’s a useful technique, even in the genomic age. A lot of you already know all about this, so apologies for preaching to the choir.


The miracle of silica gel

I put an extensive post on my own Research Blog, but here is the gist of it:

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Room Temperature RNA extraction

Derivation: The following protocol is a modified Zhao Lai et al 2006 and TRizol Plus protocol.

Expected results: I tested the protocol with Arabidopsis seedlings and it gives quality RNA that was used for RT-PCR (non-quantitative).  I am able to achieve 75-270 ng/uL (100 uL elution – take this value with a grain of salt since it is derived from the nanodrop) of RNA from 38-48 mg of seedlings (this is approximately 20 seedlings grown for 18 days). I have yet to experience a failed RT-PCR with RNA isolated using this extraction.

Keys to success: Yield is highly linked to tissue mass and quality of tissue grind. The range of tissue mass is very small. One should use a small tissue amount and process a given sample over a column many times. Tissue is ground successfully only when it is not visible in the trizol/tissue/bead mixture. Minimize RNAse paranoia – Guanidine isothiocyanate does a good job of destroying protein structure, inactivating RNAses.

More after the jump Continue reading

Bioanalyzer – RNA (Kristin)

Running a RNA Nano chip is very similar to running a DNA chip on the Bioanalyzer. However there are some things to keep in mind:

1. Clean everything with RNAse Away! before you start. I clean the chip loading stand as well as everything I am working with.

2. Make sure the reagents are at room temperature before you start to make the gel.

3. Before loading the chip, pipette 1.2 uL of each sample as well as the ladder into PCR tubes and incubate in the thermocycler for 2 minutes.

On the last point, I aliquot my samples into the PCR tubes and incubate them right before I load the gel. The instructions say to denature all the ladder in one go, but I have had better results when I denature an aliquot with my samples right before I run the chip.

Attached is a chip of 12 conifer leaf tissue extractions that worked out pretty well.

Conifer RNA Chip