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The remaining 5.460 cDNAs were thus estimated to cover around 4.036 gene transcripts yielding approximately 19.867 gene transcripts in total.
RT-PCR with primers specific for PRAT satellite DNA revealed the presence of transcripts in total RNA isolated from P. ratzeburgii adults, larvae and pupae (Fig. 1a).
A similar variability was detected for long sense transcripts in total and polysomal RNA preparations of the same tissue (Figure 7).
We first demonstrated, using RT-PCR, that mRNAs encoding "renal cystic" proteins are expressed in the OE. Figure 1A D demonstrates the expression of PC1, PC2, MKS1 and MKS3 transcripts in total RNA extracts from the OE.
A similar tendency was observed, although at a more pronounced level, for polyadenylated RNA pools where heat treatment resulted in a 30-fold increase of rpl2 transcripts in total RNA preparation.
The absolute quantification of SIV Gag, TNF-α and RPL13A transcripts in total RNA from left ventricle and spleen specimens was conducted using TaqMan probes and TaqMan One-Step RT-PCR master mix reagents (Applied Biosystems, Foster City, CA) on an ABI Prism 7700 thermal cycler (Applied Biosystems).
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Whilst the above results were performed in IVT RNAs, detecting and mapping RNA G4 within a specific transcript in total cellular RNA is more challenging.
We detected Ucp2 transcript in total hind limb skeletal muscle using real-time PCR, but at levels 30 times lower than in spleen or lung, with no significant difference between WT and Ucp3KO (results not shown).
The average representation level for all LongSAGE tags corresponding to each sense transcript in this set (3,617 transcripts expressed in total) is 45 tags per million (tpm), whereas for transcripts identified by both methods the average total SAGE tag count for a transcript is 65 tpm (1,855 transcripts) and for those identified by LongSAGE only, it is 23 tpm (1,762 transcripts).
The split reads and the processed BWA alignments were combined to produce 41,011 transcript models in total; one transcript per locus.
This is despite these two animals having similar amounts of pseudogene annotation data (Table 1), and transcript data (203,785 transcript sequences in total for human, and 203,550 for mouse).
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