Open Access Highly Accessed Research article

Whole transcriptome analysis of a reversible neurodegenerative process in Drosophila reveals potential neuroprotective genes

María José Ferreiro1, Naiara Rodríguez-Ezpeleta23, Coralia Pérez4, Michael Hackenberg5, Ana María Aransay2, Rosa Barrio4* and Rafael Cantera16*

Author Affiliations

1 Developmental Neurobiology, IIBCE, Montevideo, Uruguay

2 Genome Analysis Platform, CIC bioGUNE & CIBERehd, Derio, Spain

3 Current affiliation: AZTI Tecnalia, Marine Research Division, Sukarrieta, Spain

4 Functional Genomics, CIC bioGUNE, Derio, Spain

5 Genetics Department, Granada University, Granada, Spain

6 Zoology Department, Stockholm University, Stockholm, Sweden

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BMC Genomics 2012, 13:483  doi:10.1186/1471-2164-13-483

Published: 15 September 2012

Additional files

Additional file 1:

Table S1. Sequencing parameters of the biological replicas of the studied genotypes. Genotype symbols: Wild type (WT), Heterozygous (He), Homozygous (Ho). Letters a, b and c symbolize different experiments for each genotype. Technical replicates were grouped (ie: WT16ab).

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Additional file 2:

Table S2. Differential expression analysis. baseMean (mean expression level, at the base scale, as a joint estimate from both conditions); baseMeanA (mean expression level, at the base scale, as an estimate for condition A); baseMeanB (mean expression level, at the base scale, as an estimate for condition B); foldChange (fold change from the first to the second condition); log2FoldChange (logarithm to basis 2 of the fold change); pvalue (significance of the fold change); padjusted (p values adjusted for multiple testing with the Benjamini-Hochberg procedure, which controls false discovery rate); resVarA (ratio of the single gene estimates for the base variance to the fitted value in condition A); resVarB (ratio of the single gene estimates for the base variance to the fitted value in condition B).

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Additional file 3:

Table S3. RPKM normalization of gene counts. Genotype symbols: Wild type (WT), Heterozygous (He), Homozygous (Ho). Letters a, b and c symbolize different experiments for each genotype.Technical replicates for a same genotype sample were grouped (ie: WT16ab).

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Additional file 4:

Table S4. Number of genes significantly misregulated in homozygous or heterozygous sall mutant embryos in comparison to WT. Genotype symbols: Wild type (WT), Heterozygous (He), Homozygous (Ho). Downregulated (D) or upregulated (U) genes in the second genotype with respect to the first one; E, no significant changes in expression between the two genotypes.

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Additional file 5:

Figure S1. Dosage effect of sall genes. (A) mRNA-Seq expression plot for arm, Fas-3, Nrg, Fas2, CadN and N genes in heterozygous (He) and homozygous (Ho) sall mutant embryos at stage 16 showed consistent results with the differences in protein levels observed by Cantera et al. (Cantera et al. 2002). Notice that heterozygous sall mutant embryos have higher transcript levels than homozygous for all these adhesion and cytoskeleton genes, suggesting a dosage effect of Sall. (B) mRNA-Seq analysis of the transcriptome of WT16, He16 and Ho16 embryos, showed that five genes are differentially expressed (p < 0.01) between all the genotypes compared at stage 16 and have intermediate levels of expression in He16. (C) At stage 17, instead, four of the genes that are differentially expressed (p < 0.01) between all the genotypes compared at this stage had intermediate levels of expression in He17.

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Additional file 6:

Figure S2. Reads mapped along IM3 and dro5 genes. (A, B) 36 or 38 long reads represented by grey lines map on dro5 (A) or IM3 (B) genes. Gene, mRNA and coding sequence (CDS) are represented on the upper part of each figure. On the left, the different biological replicates of each genotype analyzed are indicated.

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Additional file 7:

Figure S3. Putative Sall binding sites in regulated genes. Graphical representation of dro5 (A) and IM3 (B) genes and the putative Sall binding sites (pink box in A, green and blue boxes in B) in the genomic region. Conservation of these sequences in various Drosophila species is depicted below the graphs.

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Additional file 8:

Table S5. Misregulated genes in homozygous sall mutant embryos. Genotype symbols: Wild type (WT), Heterozygous (He), Homozygous (Ho). Downregulated (D) or upregulated (U) genes in the second genotype with respect to the first one; E, no significant changes in expression between the two genotypes. Genes previously associated with neurodegeneration/neuroprotection are indicated in RED.

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Additional file 9:

Unbiased Gene Ontology analysis of the genes significantly misregulated in homozygous sall mutant embryos using the VLAD online tool. Genes misregulated in homozygous sall mutant embryos at stage 16, 17 and at the transition between both stages (genotype comparisons: WT16 vs Ho16; WT17 vs Ho17; Ho16 vs Ho17).

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Additional file 10:

Table S6. Functional classification of genes misregulated in homozygous sall mutant embryos with respect to wild type embryos at stage 16. Genotype comparison WT16 vs Ho16. Wild type (WT), Homozygous (Ho).Table S7. Functional classification of genes misregulated in homozygous sall mutant embryos with respect to heterozygous embryos at stage 16. Genotype comparison Ho16 vs He16. Homozygous (Ho), Heterozygous (He). Table S8. Functional classification of genes misregulated in homozygous sall mutant embryos with respect to wild type embryos at stage 17. Genotype comparison WT17 vs Ho17. Wild type (WT), Homozygous (Ho). Table S9. Functional classification of genes misregulated in homozygous sall mutant embryos with respect to heterozygous embryos at stage 17. Genotype comparison Ho17 vs He17. Homozygous (Ho), Heterozygous (He). Table S10. Functional classification of genes misregulated in homozygous sall mutant embryos at the transition from stage 16 to 17. Genotype comparison Ho16 vs Ho17. Homozygous (Ho). Table S11. Functional classification of genes misregulated in wild type embryos at the transition from stage 16 to 17. Genotype comparison WT16 vs WT17. Wild type (WT).

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Additional file 11:

Figure S4. Functional classification of misregulated genes. (A-C) Graphic representation of the main functional groups enriched in misregulated genes in the indicated genotypes, expressed as percentage of genes in each group. In red are marked the groups significantly overrepresented with respect to the total Drosophila genome with p < 0.01 and in green with p < 0.05. (A) Classification of the genes misregulated in Ho16 compared with He16. (B) Classification of the genes misregulated in Ho17 compared to He17. (C) Classification of the genes misregulated in WT embryos at the transition from stage 16 to 17.

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Additional file 12:

Table S12. Genes regulated by Sall both in embryonic stages and in and pupal muscle.

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Additional file 13:

Table S13. Oligonucleotides used for PCR analysis.

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Additional file 14:

Table S14. Functional Groups reference list. *GO categories constructed from specific literature sources.

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