65 research outputs found
Protocol Dependence of Sequencing-Based Gene Expression Measurements
RNA Seq provides unparalleled levels of information about the transcriptome including precise expression levels over a wide dynamic range. It is essential to understand how technical variation impacts the quality and interpretability of results, how potential errors could be introduced by the protocol, how the source of RNA affects transcript detection, and how all of these variations can impact the conclusions drawn. Multiple human RNA samples were used to assess RNA fragmentation, RNA fractionation, cDNA synthesis, and single versus multiple tag counting. Though protocols employing polyA RNA selection generate the highest number of non-ribosomal reads and the most precise measurements for coding transcripts, such protocols were found to detect only a fraction of the non-ribosomal RNA in human cells. PolyA RNA excludes thousands of annotated and even more unannotated transcripts, resulting in an incomplete view of the transcriptome. Ribosomal-depleted RNA provides a more cost-effective method for generating complete transcriptome coverage. Expression measurements using single tag counting provided advantages for assessing gene expression and for detecting short RNAs relative to multi-read protocols. Detection of short RNAs was also hampered by RNA fragmentation. Thus, this work will help researchers choose from among a range of options when analyzing gene expression, each with its own advantages and disadvantages
Does plantation forestry restore biodiversity or create green deserts? A synthesis of the effects of land-use transitions on plant species richness
Lordotic Deformation and Abnormal Development of Swim Bladders in Some Hatchery-Bred Marine Physoclistous Fish in Japan
Intraductal tubular adenomas (pyloric gland-type) of the pancreas: clinicopathologic features are similar to gastric-type intraductal papillary mucinous neoplasms and different from intraductal tubulopapillary neoplasms
Mitochondrial Polyadenylation Is a One-Step Process Required for mRNA Integrity and tRNA Maturation
Factors Affecting Changes in a Landscape Structure Dominated by Both Primary and Coppice Forests in the Fagus crenata
- …