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Up until recently, it has only been possible to examine a small number of transcripts over a wide range of expression levels using qPCR or a large number of transcripts over a narrower range of expression levels using microarrays.
Generally, GP distributions fit sequence count data better than NB distributions on transcripts over a wide range of relative abundance in RNA-Seq experiments (Fig. 2).
In addition, we determined that Actichip has the potential to identify transcripts over a biologically meaningful range including high, intermediate and rare abundance classes of RNAs.
The high-throughput of next-generation sequencing allows for profiling of transcripts over a wide range of abundance [ 30], providing an accurate picture of differential expression across tissues within an organism.
On the other hand, under-representation of UTRs may reflect weaker evolutionary conservation of these regions, resulting in a lack of sequence similarity (including possible UTR length differences between mouse and bank vole) to mouse transcripts over a substantial portion of contig/singleton (CS) length.
PRC1 repression of active PRC targets was further validated by qRT-PCR of single-gene transcripts over a Ring1B knockout time course; these include important genes for ESC biology (Hmga2, Tbx3, and Hdac2), development (Fzd8 and Lefty2), and metabolism (Hk1 and Eno2).
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The number of each gene-amplified product was normalized to the number of cyclophilin-A amplified product and expressed as copy numbers of PHD2 transcripts over cyclophilin-A (×10−3).
These included 12 transcripts over-expressed in vagina and 8 transcripts over-expressed in skin in all three comparisons, providing a 20 transcript tissue-specific signature.
A total of 96 transcripts were found differentially expressed in multiple strains including 17 and 20 transcripts over- and under transcribed in all strains respectively.
The transcripts over-expressed in sDCs were enriched for metabolic processes, including metabolism of nitrogen compounds and RNA, while the transcripts over-expressed in vDCs were enriched for immune-related biological processes, including defense response, phagocytosis and cell adhesion.
To the best of our knowledge, no studies to date (in vivo, ex vivo, or in vitro) have compared the number and the type of differentially expressed transcripts over such a wide absorbed-dose range.
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