Open Access Highly Accessed Research article

Somatic sex-specific transcriptome differences in Drosophila revealed by whole transcriptome sequencing

Peter L Chang1, Joseph P Dunham1, Sergey V Nuzhdin1* and Michelle N Arbeitman12*

Author Affiliations

1 Section of Molecular and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, California 90089, USA

2 Department of Biomedical Sciences, College of Medicine, Florida State University, Tallahassee, Florida 32306, USA

For all author emails, please log on.

BMC Genomics 2011, 12:364  doi:10.1186/1471-2164-12-364

Published: 14 July 2011

Additional files

Additional file 1:

Mapping statistics. Mapping statistics for all technical replicates analyzed in the experiment, including number of reads, percent mapped, sequencing coverage.

Format: XLSX Size: 15KB Download file

Open Data

Additional file 2:

Genes covered in at least one genotype. 9,473 genes covered in at least one genotype.

Format: XLSX Size: 4.6MB Download file

Open Data

Additional files 3:

Dot plots of FPKM between replicates for female, male and transformer RNA-seq data. Dot plots of FPKM between replicates in log scale for female, male and transformer RNA-seq data. R2 ranges between 0.93 and 0.96. Biological replicates are the following pairs 1 and 2, 3 and 4, and 5 and 6.

Format: PDF Size: 2.4MB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional files 4:

Dot plots of FPKM between replicates for female, male and transformer RNA-seq data. Dot plots of FPKM between replicates in log scale for female, male and transformer RNA-seq data. R2 ranges between 0.93 and 0.96. Biological replicates are the following pairs 1 and 2, 3 and 4, and 5 and 6.

Format: PDF Size: 2.3MB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional files 5:

Dot plots of FPKM between replicates for female, male and transformer RNA-seq data. Dot plots of FPKM between replicates in log scale for female, male and transformer RNA-seq data. R2 ranges between 0.93 and 0.96. Biological replicates are the following pairs 1 and 2, 3 and 4, and 5 and 6.

Format: PDF Size: 2.2MB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 6:

Genes not covered any genotype. 5,385 genes not covered in any genotype. Genes with no reads that map in any replicate are indicated in bold.

Format: XLSX Size: 1.2MB Download file

Open Data

Additional file 7:

Gene ontology functional analysis of genes not covered in any genotype. Gene ontology functional analysis of 5,385 that are not covered in any genotype.

Format: XLSX Size: 14KB Download file

Open Data

Additional file 8:

Chromosome distribution bias for genes. Chromosome distribution bias for genes expressed, genes not covered, genes differentially expressed, and genes alternatively spliced. Boldface indicate significantly over- (blue) or underrepresented (red) based on the total number of genes in the available pool, based on a one-sided Hypergeometric Test.

Format: XLSX Size: 58KB Download file

Open Data

Additional file 9:

Average coverage distribution. Average coverage distribution along annotation unit for all gene transcripts covered, shown from 5' (left) to 3' (right) for female (red), male (blue), and tra pseudomale (black) genotypes. Introns were removed. Transcripts were broken into 50 equal-length regions and each region was normalized based on the coverage of the entire transcript.

Format: PDF Size: 2.2MB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 10:

Genes expressed in at least one genotype. 8,896 genes expressed in at least one genotype. Red indicate genes with female-biased expression. Blue indicate genes with male-biased expression.

Format: XLSX Size: 4.5MB Download file

Open Data

Additional file 11:

Genes expressing more than 1 isoform. 1,722 genes expressing more than 1 isoform. Bold indicate genes downstream of tra.

Format: XLSX Size: 440KB Download file

Open Data

Additional file 12:

Comparison of junction coverage with transcript isoform FPKM. Comparison of junction coverage with transcript isoform FPKM, for female (R2 = 0.70), male (R2 = 0.73), and tra pseudomale (R2 = 0.74) genotypes.

Format: PDF Size: 1.6MB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 13:

Isoforms expressed among 1,722 genes. 4,368 isoforms expressed among 1,722 genes. Red indicate genes with female-biased expression. Blue indicate genes with male-biased expression.

Format: XLSX Size: 2.3MB Download file

Open Data

Additional file 14:

Average coverage distribution of constitutive introns. Average coverage distribution of constitutive introns along full annotation unit for 1,722 genes expressing more than one isoform transcript, shown from 5' (left) to 3' (right) for female (red), male (blue), and tra pseudomale (black) genotypes. Each gene was broken into 50 equal-length regions and each region was normalized based on the coverage of the entire gene.

Format: PDF Size: 3.6MB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 15:

Average coverage distribution of constitutive exons. Average coverage distribution of constitutive exons along full annotation unit for 1,722 genes expressing more than one isoform transcript, shown from 5' (left) to 3' (right) for female (red), male (blue), and tra pseudomale (black) genotypes. Each gene was broken into 50 equal-length regions and each region was normalized based on the coverage of the entire gene.

Format: PDF Size: 3MB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 16:

Average coverage distribution of cassette exons. Average coverage distribution of cassette exons along full annotation unit for 1,722 genes expressing more than one isoform transcript, shown from 5' (left) to 3' (right) for female (red), male (blue), and tra pseudomale (black) genotypes. Each gene was broken into 50 equal-length regions and each region was normalized based on the coverage of the entire gene.

Format: PDF Size: 3.6MB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 17:

Average fold-change between female and male for constitutive exons, cassette exons, and constitutive introns. Average fold-change between female and male for constitutive exons, cassette exons, and constitutive introns along full annotation unit for 1,722 genes expressing more than one isoform transcript, shown from 5' (left) to 3' (right). Each gene was broken into 50 equal-length regions and each region was normalized based on the coverage of the entire gene.

Format: PDF Size: 1.2MB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 18:

Coverage distribution of constitutive exons, cassette exons, and constitutive introns of varying lengths for genes expressing more than one isoform transcript. Coverage distribution of constitutive exons, cassette exons, and constitutive introns of varying lengths for 1,722 genes expressing more than one isoform transcript for female (red) and male (blue).

Format: PDF Size: 3.3MB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 19:

Average fold-change between female and male for constitutive exons, cassette exons, and constitutive introns of varying lengths for genes expressing more than one isoform transcript. Average fold-change between female and male for constitutive exons, cassette exons, and constitutive introns of varying lengths for 1,722 genes expressing more than one isoform transcript.

Format: PDF Size: 2.4MB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 20:

Genes with Tra binding sites. 10 genes with Tra binding sites.

Format: XLSX Size: 64KB Download file

Open Data

Additional file 21:

Isoforms for genes that have the Tra binding site. Isoforms for the 10 genes that have the Tra binding site. It should be noted that the location of the Tra binding site relative to each isoform is not shown.

Format: XLSX Size: 130KB Download file

Open Data

Additional file 22:

Genes identified de novo. 169 genes found between known annotated genes (NCUFF genes). 651 genes found overlapping previously annotated genes are also included (CUFF genes).

Format: XLSX Size: 379KB Download file

Open Data