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Evaluating whole transcriptome amplification for gene profiling experiments using RNA-Seq

Overview of attention for article published in BMC Biotechnology, July 2015
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About this Attention Score

  • Above-average Attention Score compared to outputs of the same age (57th percentile)

Mentioned by

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6 tweeters

Citations

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19 Dimensions

Readers on

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62 Mendeley
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Title
Evaluating whole transcriptome amplification for gene profiling experiments using RNA-Seq
Published in
BMC Biotechnology, July 2015
DOI 10.1186/s12896-015-0155-7
Pubmed ID
Authors

Sheena L Faherty, C Ryan Campbell, Peter A Larsen, Anne D Yoder

Abstract

RNA-Seq has enabled high-throughput gene expression profiling to provide insight into the functional link between genotype and phenotype. Low quantities of starting RNA can be a severe hindrance for studies that aim to utilize RNA-Seq. To mitigate this bottleneck, whole transcriptome amplification (WTA) technologies have been developed to generate sufficient sequencing targets from minute amounts of RNA. Successful WTA requires accurate replication of transcript abundance without the loss or distortion of specific mRNAs. Here, we test the efficacy of NuGEN's Ovation RNA-Seq V2 system, which uses linear isothermal amplification with a unique chimeric primer for amplification, using white adipose tissue from standard laboratory rats (Rattus norvegicus). Our goal was to investigate potential biological artifacts introduced through WTA approaches by establishing comparisons between matched raw and amplified RNA libraries derived from biological replicates. We found that 93% of expressed genes were identical between all unamplified versus matched amplified comparisons, also finding that gene density is similar across all comparisons. Our sequencing experiment and downstream bioinformatic analyses using the Tuxedo analysis pipeline resulted in the assembly of 25,543 high-quality transcripts. Libraries constructed from raw RNA and WTA samples averaged 15,298 and 15,253 expressed genes, respectively. Although significant differentially expressed genes (P < 0.05) were identified in all matched samples, each of these represents less than 0.15% of all shared genes for each comparison. Transcriptome amplification is efficient at maintaining relative transcript frequencies with no significant bias when using this NuGEN linear isothermal amplification kit under ideal laboratory conditions as presented in this study. This methodology has broad applications, from clinical and diagnostic, to field-based studies when sample acquisition, or sample preservation, methods prove challenging.

Twitter Demographics

The data shown below were collected from the profiles of 6 tweeters who shared this research output. Click here to find out more about how the information was compiled.

Mendeley readers

The data shown below were compiled from readership statistics for 62 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
United States 3 5%
Chile 1 2%
China 1 2%
Switzerland 1 2%
Unknown 56 90%

Demographic breakdown

Readers by professional status Count As %
Researcher 18 29%
Student > Ph. D. Student 15 24%
Student > Master 6 10%
Student > Bachelor 4 6%
Professor 4 6%
Other 9 15%
Unknown 6 10%
Readers by discipline Count As %
Agricultural and Biological Sciences 25 40%
Biochemistry, Genetics and Molecular Biology 14 23%
Engineering 3 5%
Environmental Science 2 3%
Medicine and Dentistry 2 3%
Other 5 8%
Unknown 11 18%

Attention Score in Context

This research output has an Altmetric Attention Score of 3. This is our high-level measure of the quality and quantity of online attention that it has received. This Attention Score, as well as the ranking and number of research outputs shown below, was calculated when the research output was last mentioned on 05 August 2015.
All research outputs
#7,463,719
of 22,818,766 outputs
Outputs from BMC Biotechnology
#427
of 935 outputs
Outputs of similar age
#88,833
of 263,145 outputs
Outputs of similar age from BMC Biotechnology
#19
of 25 outputs
Altmetric has tracked 22,818,766 research outputs across all sources so far. This one is in the 44th percentile – i.e., 44% of other outputs scored the same or lower than it.
So far Altmetric has tracked 935 research outputs from this source. They typically receive more attention than average, with a mean Attention Score of 7.8. This one is in the 37th percentile – i.e., 37% of its peers scored the same or lower than it.
Older research outputs will score higher simply because they've had more time to accumulate mentions. To account for age we can compare this Altmetric Attention Score to the 263,145 tracked outputs that were published within six weeks on either side of this one in any source. This one has gotten more attention than average, scoring higher than 57% of its contemporaries.
We're also able to compare this research output to 25 others from the same source and published within six weeks on either side of this one. This one is in the 24th percentile – i.e., 24% of its contemporaries scored the same or lower than it.