The oligonucleotide primers, used for evaluating the transcript levels of ABA1, ABA2, ABI1, ABI2, ABI3, ABI4, ABI5, RD20A, RD29B, CBF1, CBF2, CBF3, COR15A, in the real-time RT-PCR experiments, were applied as Ding et al. [33].
In a previous study evaluating the transcript profiling of peripheral mononuclear blood cells obtained from T1D, T2D and GDM patients we showed that the gene profile of T1D patients was closer to GDM than to T2D.
When evaluating the transcripts with more than ten SNPs for GO annotation, the gene percentage in each category was in proportion with the overall transcriptome GO annotation (Additional file 1: Figure S5), indicating no particular set of genes were enriched regarding SNP frequency.
In order to compensate for small differences in reverse transcription efficiency, we also evaluated the transcript levels for two endogenous controls in the samples under study.
As part of our evaluation of ZFP36 polymorphisms in humans, we have evaluated the transcript levels for all three family members in one human cell type, purified and cultured monocytes prepared from normal subjects and subjected to stimulation with LPS.
To find out whether Wolbachia-mediated downregulation of AeCHD7 is gender specific, we evaluated the transcript levels of AeCHD7 in 4-day-old female and male Ae. aegypti mosquitoes with and without Wolbachia infection.
To investigate whether the expression of csg genes is affected by loss of DnaK, we evaluated the transcript levels of csgA and csgD encoded by the csgBAC and csgDEFG operons, respectively (Fig. 2a), by real-time PCR analysis.
To evaluate the transcript abundance, Bowtie (v1.0.0) and RSEM (v1.2.15) were used for sequence alignment and calculation of TPM (Transcripts Per Million) and FPKM (Fragments Per Kilobase of transcript per Million mapped reads) (Langmead et al. 2009; Li and Dewey 2011).
To evaluate the transcript accumulation, the HS were applied on the 13th day at 1 mg C L−1 for 24 h to two different control solutions: a complete nutrient solution (see above) and a nutrient solution N-deprived, where N sources KNO3 and Ca(NO3 2 4H2O were replaced with KCl and CaCl2*2H2O at the same concentrations.
To reveal the association of grouper β-defensin expression with sex reversal, we firstly evaluated the transcript level in the pituitaries and gonads of groupers at different stages.
In order to visualize the temporal regulation of p57Kip2 throughout the differentiation process, we first evaluated the transcript levels of Cdkn1c gene in undifferentiated ES cells, in differentiating EBs and in fully differentiated cardiomyocytes, in both the wild-type and sik1flp/flp cells.
