Products

Links to Access Published Datasets, Genomes, Code and other  Products

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.
Fence Lizard (Sceloporus) Genome(s)

Coming soon! Contact me if you want early access!

This provides a high quality, chromosome-level, genome assembly for Sceloporus undulatus, reference assemblies for 34 other species of Sceloporus, and multiple transcriptomes.

Reference: 

Westfall, AK, RS Telemeco, MB Grizante, DS Waits, AD Clark, DY Simpson, RL Klabacka, AP Sullivan, GH, Perry, MW Sears, CL Cox, RM Cox, ME Gifford, HB John-Alder, T Langkilde, MJ Angilletta, AL Leaché, MA Tollis, K Kusumi, TS Schwartz. In Review. A high-quality genome assembly for the eastern fence lizard (Sceloporus undulatus), a reptile model for physiological and evolutionary ecology.  

Raw RNAseq Data on NCBI: Short Read Archive:

Raw and Reference Trinity blood transcriptomes (.fasta files) and the annotation files (.xlxs) for each of the six species are available in Dryad:

Alligator Lizard (Elgaria) Genome

Coming soon! Contact me if you want early access!

Reference: 

Clark, AC, TS Schwartz. Draft Genome Assembly of the Anguid Lizard Elgaria multicarinata (Southern Alligator Lizard)

Raw RNAseq Data on NCBI: Short Read Archive:

Raw and Reference Trinity blood transcriptomes (.fasta files) and the annotation files (.xlxs) for each of the six species are available in Dryad:

Two draft Daphnia pulicaria Genomes

Coming soon! Contact me if you want early access!

Reference: 

Clark AC, B Howell, A Wilson, TS Schwartz. Two draft Daphnia pulicaria Genomes.

Raw RNAseq Data on NCBI: Short Read Archive:

Raw and Reference Trinity blood transcriptomes (.fasta files) and the annotation files (.xlxs) for each of the six species are available in Dryad:

Reptile Blood Transcriptomes for 6 species

Reference: 

Waits, D, Simpson, D, A Sparkman, AM Bronikowski, TS Schwartz. 2019. Utility of Reptile Blood Transcriptomes in Molecular Ecology. Molecular Ecology Resources. 20:308-317. https://doi.org/10.1111/1755-0998.13110

Raw RNAseq Data on NCBI: Short Read Archive: SRP135786; SRR6841717; SRR6841722.

 

Raw and Reference Trinity blood transcriptomes (.fasta files) and the annotation files (.xlxs) for each of the six species are available in Dryad: https://doi.org/10.5061/dryad.63xsj3tz8

These transcriptomes were assembled with trinity version 2.20. The species IDs correspond to

Table 1 in the manuscript.

Schwartz, Tonia S et al. (2019), The utility of reptile blood transcriptomes in molecular ecology, v3, Dryad, Dataset, https://doi.org/10.5061/dryad.63xsj3tz8

Reptile Liver Transcriptomes from 17 species 

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.