Figure 1.
Venn diagram of transcripts detected in stallion sperm and testes by microarray analysis (SNR ≥2).
Figure 2.
Heat maps of GO functional groups for sperm up-regulated (a) and sperm down-regulated (b) transcripts.
Blue boxes denote that the gene has not been associated with the corresponding GO category. Genes with symbols in red font were validated by qRT-PCR.
Figure 3.
Validation of significantly (p<0.05) sperm up-regulated (a) and sperm down-regulated (b) genes by qRT-PCR (see also Table 1).
Table 1.
Selected most significantly (p<0.005) differentially expressed genes between stallion sperm and testes by microarray analysis and qRT-PCR (see also Fig. 3).
Figure 4.
Summary statistics for mapped RNA sequence tags
: (a) Comparison of mapped tags (AC≥1) between the two sperm samples; (b) Proportions of tags with very high (AC≥100), high (10<AC<100), and medium (1≤AC≤10) expression.
Table 2.
Summary statistics for stallion sperm RNA-seq.
Table 3.
Distribution and expression of mapped RNA sequence tags in the horse genome.
Figure 5.
Structural annotation of 19, 257 mapped RNA sequence tags (AC≥1):
(a) Distribution of the tags in structural annotation categories by ERANGE; (b) Comparison of annotated genes by GOanna (human genome) and ERANGE (horse genome).
Table 4.
NCBI BLAST alignments for 12 most abundant (AC>50,000) un-annotated mapped RNA sequence tags.
Table 5.
Structural and functional annotations for mRNAs and ESTs with the highest AC values by RNA-seq.
Figure 6.
Comparison of RNA-seq data with current equine gene models:
(a) PKM2 showing 9 in silico prediction sites, of which two are positioned 5′ upstream to exon 1; (b) CRISP3 with 3 in silico prediction sites, all located 5′ upstream to exon 1; (c) PRM1 and TNP2 cluster (the protamine cluster) with 12 in silico prediction sites of which only two align with PRM1 and TNP2 exons. Black boxes with numbers –exons in current gene models; blue boxes –very highly expressed tags (AC≥100); red boxes–highly expressed tags (10<AC<100); green boxes–tags with medium expression (1≤AC≤100). Exact start and end sites of all mapped tags are presented in Additional file 7.
Figure 7.
ECAY transcripts in stallion sperm.
Agarose gel images showing RT-PCR amplicons of 7 ECAY genes and transcripts in stallion sperm.