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Supplemental Information

Table S1. Highly expressed genes and GO analyses

Comparison of 500 highest expressed genes among stages and Gene Ontology analysis

DOI: 10.7287/peerj.preprints.2782v1/supp-1

Table S2. Differentially expressed genes

Result of differentially expression analysis. Gene ontology of stage specific DEGs

DOI: 10.7287/peerj.preprints.2782v1/supp-2

Table S3. Oxidative metabolism

Normalized read counts of Krebs cycle and respiratory chain genes

DOI: 10.7287/peerj.preprints.2782v1/supp-3

Table S4. Antioxidant genes

Normalized read counts of antioxidant genes

DOI: 10.7287/peerj.preprints.2782v1/supp-4

Table S5. Lipid metabolism

Normalized read counts of genes related to different lipid related metabolic processes: fatty acid, steroid and phospholipid

DOI: 10.7287/peerj.preprints.2782v1/supp-5

Table S6. Carbohydrate metabolism

Normalized read counts of glycolytic and pentose phosphate pathway genes

DOI: 10.7287/peerj.preprints.2782v1/supp-6

Table S7. Protein metabolism

Normalized read counts of genes coding general protein metabolic pathways including protein degradation, protein synthesis, amino acid transport and metabolism

DOI: 10.7287/peerj.preprints.2782v1/supp-7

Table S8. New genes prediction

Characterization of putative new transcripts predicted for Dm28c. Statistical description of the validation by HMM and Blast searches

DOI: 10.7287/peerj.preprints.2782v1/supp-8

Table S9. Raw and normalized counts

Raw transcript levels from ERANGE. Normalized counts were obtained from DESeq2

DOI: 10.7287/peerj.preprints.2782v1/supp-9

Figure S1. Stage specific TS examination

Representation of predicted molecular weights of trans-sialidases specific from amastigotes (aTS, green), epimastigotes (eTS, blue) and trypomastigotes (tTS, orange). T test was performed, ** represents p-value<0.01.

DOI: 10.7287/peerj.preprints.2782v1/supp-10

Figure S2. Surface gene composition in different T. cruzi stages

A) Expression of each gene in normalized read counts is shown for the different group of membrane component. At the X axis each gene is plotted at the same order,for the three stages. B) Sum of total normalized read counts per gene Kb of each family group in the three stages. Different cycle stages are represented: amastigote (green), epimastigote (blue) and trypomastigote (orange).

DOI: 10.7287/peerj.preprints.2782v1/supp-11

Figure S3. GP63 philogeny

Neighbor-joining tree of the protein sequences of GP63 genes; numbers correspond to gene ID. Differentially up-regulated in A (green), differentially up-regulated in T (orange)

DOI: 10.7287/peerj.preprints.2782v1/supp-12

Figure S4. Gene expression patterns

Comparison to known protein expression profiles. A) flagellum associated genes down-regulated in amastigotes. B) genes related to conversion of histidine to glutamate up-regulated in epimastigotes. C) mucins up regulated in trypomastigotes.

DOI: 10.7287/peerj.preprints.2782v1/supp-13

Additional Information

Competing Interests

The authors declare that they have no competing interests.

Author Contributions

Luisa Berná conceived and designed the experiments, performed the experiments, analyzed the data, wrote the paper, prepared figures and/or tables, reviewed drafts of the paper.

Maria Laura Chiribao conceived and designed the experiments, performed the experiments, analyzed the data, contributed reagents/materials/analysis tools, wrote the paper, prepared figures and/or tables, reviewed drafts of the paper.

Gonzalo Greif performed the experiments, analyzed the data, contributed reagents/materials/analysis tools, reviewed drafts of the paper.

Matias Rodriguez analyzed the data, reviewed drafts of the paper.

Fernando Alvarez-Valin analyzed the data, wrote the paper, reviewed drafts of the paper.

Carlos Robello conceived and designed the experiments, analyzed the data, contributed reagents/materials/analysis tools, wrote the paper, reviewed drafts of the paper.

DNA Deposition

The following information was supplied regarding the deposition of DNA sequences:

The raw squences are not publicly available yet, but are available at:

https://mega.nz/#F!cMVUmCLD

key: 3Crp4y26SBscGtTI0r21SA

Also the same raw sequences were deposited at the NCBI database under SRA accession number SRP072022 that will be available with the publication of the paper.

Data Deposition

The following information was supplied regarding data availability:

The raw data included in the manuscript are the count of mapped reads in each transcript. The raw counts and normalized counts of transcripts are presented in Supplementary Table S9.

Funding

This work was supported by Agencia Nacional de Investigación e Innovación (Uruguay) grant DCI-ALA/2011/023-502 “Contrato de apoyo a las políticas de innovación y cohesión territorial”, and FOCEM (MERCOSUR Structural Convergence Found) COF 03/11, and research fellowships from ANII-Uruguay (MLC, GG). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.


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