Links to Access Published Data and Code
Please use the links below to access all of our repositories for code and data. For data and code from specific projects, please see the links on Research Project pages or Publications.
GITHUB for code:
Reptile Transcriptomes from 17 species (Liver)
McGaugh SE, Bronikowski AM, Kuo C-H, Reding DM, Addis EA, Flagel LE, Janzen FJ, Schwartz TS: Rapid molecular evolution across amniotes of the IIS/TOR network. PNAS 2015.
Transcriptome Assemblies, Annotation, Alignments, etc on dryad: http://dx.doi.org/10.5061/dryad.vn872
IMAGE: Representatives of the 66 species whose transcriptomes/genomes were used to study the evolution of the Insulin- Insulin-like signaling / Target of Rapamycin (IIS/TOR) molecular network across amniotes (mammals and reptiles/birds). This molecular network regulates lifespan, reproduction, metabolic diseases, cancer, and aging. Among amniotes, the hormones, receptors and binding proteins of IIS/TOR were found to be quickly evolving.
Photographs courtesy of: predicted reptile IGF1 and IGF1R protein structures, Tonia S. Schwartz; western terrestrial garter snake ecotypes, Stevan J Arnold; alligator, Corey Cates; cottonmouth snake, snapping turtle, David Delaney; brown anole, Dan A Warner; mallard duck, Hannah Syversen; alligator lizard, Rory Telemeco; armadillo, Tom Friedel, birdphotos.com; elephants, Beth Archie; chimpanzee, Ian Gilby; dog, Ryan Rapp; dolphin, US Fish & Wildlife; opossum, Klaus Rudloff. Composition by Tonia S. Schwartz.
Dissecting Stress Response Networks
Schwartz, TS, and AM Bronikowski. 2013. Dissecting molecular stress networks: identifying nodes of divergence between life-history phenotypes. Molecular Ecology. 22(3): 739-756 DOI: 10.1111/j.1365-294X.2012.05750.x
Raw Data on NCBI: Short Read Archive (SRA052923).
Genbank Sequences Accessions: Catalase Isoform 1, JX291960; Catalase Isoform 2, JX291961; Glutathione Peroxidase1, JX291962; Glutathione Peroxidase 3, JX291963;
Glutathione Peroxidase 4, JX291964; HSP40A1, JX291965; HSP40A4, JX291966; HSP70A1, JX291967; Superoxide dismutase 1, JX291968; Superoxide dismutase 2 Isoform 1, JX291969; Superoxide dismutase 2 Isoform 2, JX291970; Superoxide dismutase 3, JX291971.
Physiological Data: DRYAD repository, doi:10.5061/dryad.sb30r.
Cleaning Illumina Reads: http://main.g2.bx.psu.edu/u/ts-ecogen/w/groomilluminasolexatrimq20filter20bp
Mapping Illumina reads to candidate genes: http://main.g2.bx.psu.edu/u/ts-ecogen/w/map-illumina-indiv-to-candidate-transcripts-and-count
Garter Snake Transcriptome
Schwartz, TS*, H Tae*, Y Yang, K Mockaitis, JL Van Hemert, SR Proulx, J-H Choi, and AM Bronikowski. 2010. A garter snake transcriptome: pyrosequencing, de novo assembly, and sex-specific differences. BMC Genomics. 11: 694-715.
Raw Data on NCBI: Short Read Archive (SRA010134).
Transcriptome Assemblies, Annotation, Alignments, etc: The servers that had been hosting these data have been shut down. These data will soon be available from Dryad.