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A comprehensive assessment of RNA-seq protocols for degraded and low-quantity samples

Overview of attention for article published in BMC Genomics, June 2017
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About this Attention Score

  • In the top 25% of all research outputs scored by Altmetric
  • High Attention Score compared to outputs of the same age (86th percentile)
  • Good Attention Score compared to outputs of the same age and source (66th percentile)

Mentioned by

blogs
1 blog
twitter
13 tweeters

Citations

dimensions_citation
53 Dimensions

Readers on

mendeley
206 Mendeley
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1 CiteULike
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Title
A comprehensive assessment of RNA-seq protocols for degraded and low-quantity samples
Published in
BMC Genomics, June 2017
DOI 10.1186/s12864-017-3827-y
Pubmed ID
Authors

Sven Schuierer, Walter Carbone, Judith Knehr, Virginie Petitjean, Anita Fernandez, Marc Sultan, Guglielmo Roma

Abstract

RNA-sequencing (RNA-seq) has emerged as one of the most sensitive tool for gene expression analysis. Among the library preparation methods available, the standard poly(A) + enrichment provides a comprehensive, detailed, and accurate view of polyadenylated RNAs. However, on samples of suboptimal quality ribosomal RNA depletion and exon capture methods have recently been reported as better alternatives. We compared for the first time three commercial Illumina library preparation kits (TruSeq Stranded mRNA, TruSeq Ribo-Zero rRNA Removal, and TruSeq RNA Access) as representatives of these three different approaches using well-established human reference RNA samples from the MAQC/SEQC consortium on a wide range of input amounts (from 100 ng down to 1 ng) and degradation levels (intact, degraded, and highly degraded). We assessed the accuracy of the generated expression values by comparison to gold standard TaqMan qPCR measurements and gained unprecedented insight into the limits of applicability in terms of input quantity and sample quality of each protocol. We found that each protocol generates highly reproducible results (R (2) > 0.92) on intact RNA samples down to input amounts of 10 ng. For degraded RNA samples, Ribo-Zero showed clear performance advantages over the other two protocols as it generated more accurate and better reproducible gene expression results even at very low input amounts such as 1 ng and 2 ng. For highly degraded RNA samples, RNA Access performed best generating reliable data down to 5 ng input. We found that the ribosomal RNA depletion protocol from Illumina works very well at amounts far below recommendation and over a good range of intact and degraded material. We also infer that the exome-capture protocol (RNA Access, Illumina) performs better than other methods on highly degraded and low amount samples.

Twitter Demographics

The data shown below were collected from the profiles of 13 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 206 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
United Kingdom 1 <1%
United States 1 <1%
South Africa 1 <1%
Unknown 203 99%

Demographic breakdown

Readers by professional status Count As %
Researcher 56 27%
Student > Ph. D. Student 41 20%
Student > Master 20 10%
Student > Bachelor 17 8%
Other 13 6%
Other 29 14%
Unknown 30 15%
Readers by discipline Count As %
Biochemistry, Genetics and Molecular Biology 75 36%
Agricultural and Biological Sciences 50 24%
Medicine and Dentistry 12 6%
Computer Science 7 3%
Immunology and Microbiology 7 3%
Other 23 11%
Unknown 32 16%

Attention Score in Context

This research output has an Altmetric Attention Score of 14. 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 02 August 2017.
All research outputs
#1,654,956
of 17,897,867 outputs
Outputs from BMC Genomics
#540
of 9,462 outputs
Outputs of similar age
#37,936
of 280,002 outputs
Outputs of similar age from BMC Genomics
#3
of 6 outputs
Altmetric has tracked 17,897,867 research outputs across all sources so far. Compared to these this one has done particularly well and is in the 90th percentile: it's in the top 10% of all research outputs ever tracked by Altmetric.
So far Altmetric has tracked 9,462 research outputs from this source. They receive a mean Attention Score of 4.4. This one has done particularly well, scoring higher than 94% of its peers.
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 280,002 tracked outputs that were published within six weeks on either side of this one in any source. This one has done well, scoring higher than 86% of its contemporaries.
We're also able to compare this research output to 6 others from the same source and published within six weeks on either side of this one. This one has scored higher than 3 of them.