Seriatopora hystrix variable temperature study (SHVTS)

Briefly, corals from an upwelling site (Houbihu) and a non-upwelling site (Houwan) in Southern Taiwan were exposed to either upwelling-simulating (i.e, "variable;" 23-29ºC over a 6-hr period) or stable (26ºC) temperature regime for one week, and a variety of physiological and molecular-scale parameters were assessed. All data has been posted below. 

1. For the description of the original SHVTS experiment, please see this manuscript.

2. For access to the S. hystrix transcriptome, as well as a description of the experiment, please go to  

     this site. Here is a brief description of the library preparation methods. For basics on next

      generation sequencing chemistries, check out this (old!) Power Point presentation. For a huge

      fasta file of the contig sequences, please click here

3. For more molecular-scale data on this same samples, please see this manuscript.

4. There was also an interest in knowing how the transplantation out of the field and into the

      aquarium affected the experimental corals, a topic discussed in this manuscript.

5. An analysis of proteins over-expressed by samples of the stable temperature treatment relative to

    those of the variable temperature treatment can be found in this book chapter.

6. An analysis of proteins differentially concentrated between conspecifics of the two study sites,

    Houwan and Houbihu, can be found in this manuscript. The differentially concentrated proteins

    can be found in list form here

7. Finally, a large-scale comparison of the transcriptome vs. the proteome was conducted, and

     essentially zero congruency was found between gene and protein expression. The manuscript

     (Mayfield et al. 2016 Mol Ecol) can be downloaded here

My main goal now is to do more protein sequencing with nano-LC to see if the 2D+MS data are reproducible (and also to see if any additional differentially concentrated proteins are unveiled). 

A  S. hystrix  nubbin used in the SHVTS. 

A S. hystrix nubbin used in the SHVTS. 

Houbihu, the upwelling site from which half of the  S. hystrix  colonies were collected. 

Houbihu, the upwelling site from which half of the S. hystrix colonies were collected. 

near Houbihu, Nanwan, Taiwan

near Houbihu, Nanwan, Taiwan

Topside view of Houwan, the non-upwelling site

Topside view of Houwan, the non-upwelling site

Yes, there is a bunny in the tank room.

Yes, there is a bunny in the tank room.

Seriatopora hystrix  nubbins grown in suspension (they are on fishing line, not the bottom of the plastic basket). 

Seriatopora hystrix nubbins grown in suspension (they are on fishing line, not the bottom of the plastic basket). 

I have nearly published all of the data associated with this project. We even tested the physiological condition of corals in the field vs. those used in the experiments (in this manuscript). Here are the associated data files (this is a work in progress):

1. Here is a JMP file for all data for the 12 RNA-Seq samples only. The associated raw data can be

   found here

2. Field data from the sampling sites: Houbihu (upwelling) and Houwan (non-upwelling). 

       A: Houbihu and Houwan temperature data. Condensed into monthly means

       B: Wanlitong (near Houwan) light data

       C: Houbihu light data

3. Tank data. 

      A: Tank temperatures. In JMP format

      B: Light data (photosynthetically active radiation). 

      C: Light data averaged across week-long experiment in JMP format. 

      C: Light data-in situ vs. ex situ

Real-time PCR data for four Symbiodinium genes targeted as part of the first publication describing this experiment (Mayfield et al. 2012 J Exp Biol). download

For a PCA featuring all expressed mRNAs (RNA-Seq), please scroll to the interactive plot at the bottom of the page.