The two Affymetrix Latin-Square spike-in data sets (HG-U113A and HG-U95Av2) each contain several spiked-in transcripts in known locations on a set of chips.
The results show the defects of bioinformatics methods in predicting alternatively spliced transcripts on one hand.
Ms. Kennedy has liberally sprinkled her interviews with "you know" and "um," as can be seen in transcripts posted on newspaper Web sites.
To show directly that the decrease in transcripts relies on a shortening of the poly(A) tail we used the RNA ligation-mediated poly(A) test (RL-PAT) [23] of decreased (Fig. 6A) and not-changed (Fig. 6B) transcripts.
Another interesting observation is the concomitant reduction in JNK1 and increase in JNK3 transcripts on decidualization.
The decrease in HspX protein levels in Comp5 bacteria paralleled the decline in hspX transcripts on day 5 (Fig. 4C).
Potential Pax3 targets, based on changes in transcript levels on the gain of function genetic background, were validated by analysis on loss or partial loss of function Pax3 mutant backgrounds.
(A ) Analysis of alternative spliced isoforms in transcripts chosen solely on exon array data showing NOVA-dependent steady-state mRNA changes and robust HITS-CLIP clusters in introns.
By comparing the NET-seq output with a microarray of Poly(A)+ RNA, we show that for the majority (≈88%) of genes, the change in transcript levels on the GLU to GAL shift reflects altered transcription rather than altered transcript stability (Supplementary file 1A).
Although current methodologies allow characterization of the stability of individual transcripts, procedures designed to measure alterations in transcript abundance/turnover on a high throughput scale are lacking.
