The agglomerative clustering command (Agglomerate) in Mathematica v. 8.0 (Wolfram Research) was used with the Euclidean distance metric to provide a relative ordering of the transcript expression vectors.
The KEGG pathways were ranked in order of the number of transcripts assigned to each pathway in reproductive and non-reproductive SE, and the top 10 KEGG pathways were identified for each reproductive morph.
Additional serpins were identified using a synteny based approach, which relies on the conservation of the order of chromosomal transcripts between related species.
In order to localise the transcripts of onychophoran opsins we performed RT-PCR using RNA from dissected eyes and brains.
In order to locate the transcripts of two selected genes in situ, fluorescence in situ hybridization (FISH) was used.
In order to quantify the transcripts of the interest genes, real-time PCR was performed using a SYBR Green Premix Ex Taq (Takara, Japan) on ABI 7900 (ABI, USA).
In order to quantify the transcripts of the interest genes, real-time PCR was performed using a SYBR Green Premix Ex Taq (Takara, Japan) on Light Cycler 480 (Roche, Switzerland).
In order to validate the presence of the transcripts predicted by the viral microarray and to explore the sensitivity of the present assays, a number of quantitative reverse transcription real-time PCR (qRT-PCR) assays were established (see Materials and Methods) and used for detection and quantitation of selected viral RNAs in lymphnodes of cattle with MCF.
In order to evaluate the specificity of the transcripts involved in both the developmental processes studied here, i.e. meiosis and follicle formation, individual library specific ESTs were studied.
Transcriptome reconstruction was performed using uniquely mapped reads or, alternatively, all the reads (unique and repeated) in order to improve the identification of the transcripts that are duplicated in the P. profundum genome like for example the CRISP elements and to better define the transcript structure of the genes having repeated regions.
