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Data
Coral transcriptomes
Each transcriptome includes a fasta file of contig/isotig sequences plus separate lookup tables for correspondences between contigs and isogroups (i.e., genes), isogroups correspondences with gene names, GO, KOG and KEGG terms. Also provided are protein translations and corresponding coding sequences (CDS), extracted based on blastx hits to Nematostella vectensis and Acropora digitifera proteomes.
Details on annotations
acropora millepora
This transcriptome is from Moya et al. Mol Ecol 2012, 21: 2440-2454. Annotaitons by Matz.
Montipora aequituberculata
Illumina/Trinity based trancriptome from adult corals, with Symbiodinium-specific reads excluded. This transcriptome was generated in collaboration with Jeroen van de Water, Bette Willis (James Cook University, Australia), and Madeleine van Oppen (Australian Institute of Marine Science).
acropora hyacinthus
 Larval 454-based trancriptome, assembled by Eli Meyer in 2012. 
acropora cervicornis
​This transcriptome is by 
Libro et al 2013, doi:10.1371/journal.pone.0081821. Annotations by Matz.
porites astreoides
Adult 454-based trancriptome; Symbiodinium-specific reads excluded. From Kenkel, Meyer and Matz, Mol Ecol 2013, 22: 4322-4334
acropora tenuis
454-based trancriptome from larvae and Symbiodinium-free recruits post-metamorphosis, assembled by Eli Meyer in 2012. 

montastrea cavernosa
​genome
The source coral comes from the Flower Garden Banks. This assembly is based on combination of PacBio and 10x Genomics reads. The initial assembly was generated by Zach Fuller from Molly Przeworski's lab at Columbia University. See the README file included with the assembly for the assembly protocol. July 2018 versions (the redundancy-removed and the phased version) and annotations are by Yi Liao (Matz lab). The original assembly and annotations are also included (directory OLD).
Stats (July 2018 version):
​5161 sequences.
average length  :  
86.9 kb 
                       N50  :  343 kb
        total length :  
448 Mb

Code
Picture
All code written by Misha can now be obtained from his GitHub page (z0on).

In addition, there are three R packages available from CRAN:

MCMC.qPCR: Bayesian analysis of qPCR data (does not require control genes)
 - Tutorial for MCMC.qPCR package 

 - paper describing the method

KOGMWU:  Functional summaries and meta-analysis of genome-wide gene expression based on KOG class annotations, as in Dixon et al Science 2015 and Strader et al. Mol Ecol 2016.

MCMC.OTU: Bayesian analysis of OTU counts (basically MCMC.qPCR package cannibalized for metabarcoding)

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