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Selection of reference genes for diurnal and developmental time-course real-time PCR expression analyses in lettuce

Overview of attention for article published in Plant Methods, March 2016
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Title
Selection of reference genes for diurnal and developmental time-course real-time PCR expression analyses in lettuce
Published in
Plant Methods, March 2016
DOI 10.1186/s13007-016-0121-y
Pubmed ID
Authors

Tiziana Sgamma, Judith Pape, Andrea Massiah, Stephen Jackson

Abstract

Real-time quantitative polymerase chain reaction (RT-qPCR) analysis is a low cost and sensitive technique that is widely used to measure levels of gene expression. Selecting and validating appropriate reference genes for normalising target gene expression should be the first step in any expression study to avoid inaccurate results. In this study, ten candidate genes were tested for their suitability for use as reference genes in diurnal and developmental timecourse experiments in lettuce. The candidate reference genes were then used to normalise the expression pattern of the FLOWERING LOCUS T (FT) gene, one of key genes involved in the flowering time pathway whose expression is known to vary throughout the day and at different stages of development. Three reference genes, LsPP2A-1 (PROTEIN PHOSPHATASE 2A-1), LsPP2AA3 (PROTEIN PHOSPHATASE 2A REGULATORY SUBUNIT A3) and LsTIP41 (TAP42-INTERACTING PROTEIN OF 41 kDa), were the most stably expressed candidate reference genes throughout both the diurnal and developmental timecourse experiments. In the developmental experiment using just LsPP2A-1 and LsTIP41 as reference genes would be sufficient for accurate normalisation, whilst in the diurnal experiment all three reference genes, LsPP2A-1, LsPP2AA3 and LsTIP41, would be necessary. The FT expression pattern obtained demonstrates that the use of multiple and robust reference genes for RT-qPCR expression analyses results in a more accurate and reliable expression profile. Reference genes suitable for use in diurnal and developmental timecourse experiments in lettuce were identified and used to produce a more accurate and reliable analysis of lsFT expression levels than previously obtained in such timecourse experiments.

Twitter Demographics

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Mendeley readers

The data shown below were compiled from readership statistics for 43 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Chile 1 2%
United States 1 2%
Unknown 41 95%

Demographic breakdown

Readers by professional status Count As %
Student > Ph. D. Student 15 35%
Researcher 7 16%
Student > Master 7 16%
Student > Bachelor 6 14%
Student > Doctoral Student 1 2%
Other 0 0%
Unknown 7 16%
Readers by discipline Count As %
Agricultural and Biological Sciences 28 65%
Biochemistry, Genetics and Molecular Biology 6 14%
Environmental Science 1 2%
Engineering 1 2%
Unknown 7 16%

Attention Score in Context

This research output has an Altmetric Attention Score of 1. 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 04 April 2016.
All research outputs
#3,861,403
of 7,492,829 outputs
Outputs from Plant Methods
#156
of 239 outputs
Outputs of similar age
#147,963
of 272,154 outputs
Outputs of similar age from Plant Methods
#6
of 8 outputs
Altmetric has tracked 7,492,829 research outputs across all sources so far. This one is in the 27th percentile – i.e., 27% of other outputs scored the same or lower than it.
So far Altmetric has tracked 239 research outputs from this source. They typically receive a little more attention than average, with a mean Attention Score of 5.5. This one is in the 20th percentile – i.e., 20% 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 272,154 tracked outputs that were published within six weeks on either side of this one in any source. This one is in the 35th percentile – i.e., 35% of its contemporaries scored the same or lower than it.
We're also able to compare this research output to 8 others from the same source and published within six weeks on either side of this one. This one has scored higher than 2 of them.