Capabilities and Resources

ORNL ENIGMA Capabilities Developed

1. Enhanced protocols for the simultaneous extraction and purification of intact and high molecular weight DNA and RNA from high Fe and humic acid clays.
2. New protocol for the closure of high G+C DNA sequence gaps between contigs for “discontiguous finished genomes”.
3. Slow-flow and long-term continuous cultivation techniques for studying whole microbial community succession, responses to perturbations, attaining enriched and simplified consortia, and isolating individual species from the field.
4. Development of controlled cultivation techniques simultaneous cultivation and perturbation of dissimilar organisms to attain model microbial communities.
5. Multi-species microarrays on a single 12X Nimblegen slide with <1% cross hybridization.
6. Fluorescent poly- and mono- clonal antibodies for species identification in consortia.
7. Enhanced analytical techniques for Illumina metagenomic and metatranscriptomic datasets.

Cultivation

  • Aerobic and anaerobic small volume batch cultivation (0.2mL-2L).
  • Controlled cultivation; batch, fed batch and continuous flow (0.2L-5L) using New Brunswick Scientific Bioflo110 1.3 L and 7.5 L fermenters.
  • High-throughput screening of aerobic and anaerobic cultures (up to 200 simultaneously); Bioscreen C.
Model microbial community cultivation in New Brunswick Scientific Bioflo110 1.3L and 7.5L fermenters. bioreactor
Model microbial community cultivation in New Brunswick Scientific Bioflo110 1.3L and 7.5L fermenters. Natural microbial community cultivation and enrichment in custom designed bioreactors for enriched consortia and isolation of new keystone species.


Systems Biology

  • Clean-room facilities for in-house microarray fabrication.
  • Laboratories for microarray data generation and analysis

 

Equipment includes

Nimblegen 12-bay hybridization station, automated array washing system and 2um-resolution scanner for high-density DNA microarrays.

 

Software includes

NimbleScan, SignalMap, JMP Genomics, Pathway tools and KnowledgeBases
  • Next-Generation DNA Sequencing

 

Equipment includes

GS FLX running Titanium chemistry (454 Life Sciences), GAIIx and HiSeq2000 (Illumina) instruments. In addition, two ABI 3730xl 96-plate based DNA sequencers are available.

 

Software includes

A variety of software are being used and on an available cluster and being assessed.
454 Illumina HiSeq 2000
454 Life Sciences GS FLX+ System with titanium chemistry generates read lengths up to 1 kb. Illumina HiSeq 2000 sequencing system generates up to 600 Gb of DNA per run.