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: https://github.com/tschwart/Schwartz_Lab
Reptile Transcriptomes from 17 species (Liver)

Reference: 

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.

doi: 10.1073/pnas.1419659112​

 

Raw Data on NCBI: Short Read Archive SRA062458 and SRP017466.

 

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

 

Reference: 

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.

 

Galaxy Workflows. 

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

 

Reference: 

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.

 

 

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