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DNA extraction methodologies 

Original Global Rumen Census documentation; Project scope and Protocols v. 5 (by Drs Gemma Henderson and Peter Janssen.  pdf Global Rumen Census Project Overview... (0.67MB) 

Rumen Microbial DNA extraction methodologies taken from document above.  pdf GRC DNA extraction methods.pdf (0.32MB) 


Amplicon sequencing pipelines

Kittlemann et al. 2013. PLoS ONE, 8: e47879. pdf journal.pone.0047879[1].pdf (0.66MB) 
Multiplex 454 Titanium pyrosequencing. Supplementary information

Summary scheme for pipeline; kindly provided by Sandra Kittelmann pdf Summary scheme.pdf (0.19MB) 

Multistep scheme for pipeline; kindly provided by Sandra Kittelmann pdf Full scheme.pdf (0.20MB) 

QIIME: tutorials site

Emulsion-based clonal amplification of DNA manual for Roche GS FLX+ pdf Roche manual (2.04MB) 


Metagenome dataset links

Hess et al. 2011. Science 331: 463-467. Bioproject Metagenome dataset

Brulc et al. 2009. Proc Natl Acad Sci USA 106: 1948-1953. Bioproject Metagenome dataset steer 8 (01), steer 64 (02), steer 71 (03), dataset from pooled sample of steers 8, 64 and 71 (04).   


Publicly available genome sequences from rumen bacteria and archaea

Table kindly supplied by Bill Kelly. pdf Genome Table March2014.pdf (0.35MB) 


 General links

 Science databases/tools

NCBI     National Centre for Biotechnology Information
CAZy  Carbohydrate Active Enzymes
KEGG  Kyoto Encyclopedia of Genes and Genomes
Pfam  Protein Family Database
SignalP  Signal Peptide Cleavage finder
TMHMM  Prediction of transmembrane helices in proteins
IMG/M  Integrated Microbial Genomes (with microbiome samples)
GOLD  Genomes Online Database
RDP  Ribosomal Database Project
greengenes  16S rRNA gene database
HMMER  Hidden Markov Model search
SMART  Simple Modular Architecture Research Tool
Superfamily  HMM library and genome assignments server
   
  Science Bodies/Networks
Animal Selection Genetics and Genomics Network
AgResearch Limited
Global Research Alliance
Livestock Research Group
Livestock Emissions and Abatement Research Network (LEARN)
New Zealand Agricultural Greenhouse Gas Centre
Feed and Nutrition Network and Database
Itzik Mizrahi Lab, Volcani Centre, Israel

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