RNAseq by Total RNA Library Identifies Additional RNAs Compared to Poly(A) RNA Library

Guo, Yan; Zhao, Shilin; Sheng, Quanhu; Guo, Mingsheng; Lehmann, Brian D.; Pietenpol, Jennifer A.; Samuels, David C.; Shyr, Yu

doi:10.1155/2015/862130

Cited by 42 publications

(33 citation statements)

References 37 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Finally, we suspect that strategies employing enrichment of polyadenylated transcripts introduce biases as well. Differences in poly(A) tail length may very well affect the efficiency of poly(T)-primed reverse transcription 33 .…”

Section: Discussionmentioning

confidence: 99%

Efficient and specific oligo-based depletion of rRNA

Kraus

Brink

Siegel

2019

Preprint

View full text Add to dashboard Cite

In most organisms, ribosomal RNA (rRNA) contributes to >85% of total RNA. Thus, to obtain useful information from RNA-sequencing (RNA-seq) analyses at reasonable sequencing depth, typically, mature polyadenylated transcripts are enriched or rRNA molecules are depleted. Targeted depletion of rRNA or other highly abundant transcripts is particularly useful when studying transcripts lacking a poly(A) tail, such as some non-coding RNAs (ncRNAs), most bacterial RNAs and partially degraded or immature transcripts. While several commercially available kits allow effective rRNA depletion, their efficiency relies on a high degree of sequence homology between oligonucleotide probes and the target RNA. This restricts the use of such kits to a limited number of organisms with conserved rRNA sequences.In this study we describe the use of biotinylated oligos and streptavidin-coated paramagnetic beads for the efficient and specific depletion of trypanosomal rRNA. Our approach reduces the levels of the most abundant rRNA transcripts to less than 5% with minimal off-target effects.By adjusting the sequence of the oligonucleotide probes, our approach can be used to deplete rRNAs or other abundant transcripts independent of species. Thus, our protocol provides a useful alternative for rRNA removal where enrichment of polyadenylated transcripts is not an option and commercial kits for rRNA are not available.

show abstract

Section: Discussionmentioning

confidence: 99%

Efficient and specific oligo-based depletion of rRNA

Kraus

Brink

Siegel

2019

Preprint

View full text Add to dashboard Cite

show abstract

“…Ribosomal removal methods address these issues by directly depleting the rRNA while leaving other transcripts intact. This technique is widely utilized and is a basic component of many large datasets (Cui et al 2010;Zhao et al 2014;Guo et al 2015).…”

Section: Introductionmentioning

confidence: 99%

Cross-Site Comparison of Ribosomal Depletion Kits for Illumina RNAseq Library Construction

Herbert

Kershner

Butty

et al. 2017

Preprint

View full text Add to dashboard Cite

Ribosomal RNA (rRNA) comprises at least 90% of total RNA extracted from mammalian tissue or cell line samples. Informative transcriptional profiling using massively parallel sequencing technologies requires either enrichment of mature poly-adenylated transcripts or targeted depletion of the rRNA fraction. The latter method is of particular interest because it is compatible with degraded samples such as those extracted from FFPE and also captures transcripts that are not poly-adenylated such as some non-coding RNAs. Here we provide a cross-site study that evaluates the performance of ribosomal RNA removal kits from Illumina, Takara/Clontech, Kapa Biosystems, Lexogen, New England Biolabs and Qiagen on intact and degraded RNA samples. We find that all of the kits are capable of performing significant ribosomal depletion, though there are differences in their ease of use. All kits were able to remove ribosomal RNA to below 20% with intact RNA and identify ∼14,000 protein coding genes from the Universal Human Reference RNA sample at >1FPKM. Analysis of differentially detected genes between kits suggests that transcript length may be a key factor in library production efficiency. These results provide a roadmap for labs on the strengths of each of these methods and how best to utilize them.

show abstract

“…One of the primary minable yet underutilized products of RNAseq data is lncRNA. Based on previous findings (Guo, 2015), total RNAseq produces data better suited for studying lncRNA than RNAseq data produced from a poly(A) RNA library. Taking advantage of the unique properties of total RNAseq, we profiled lncRNA expression in the mouse auditory forebrain at four postnatal time points (postnatal days P7, P14, P21, and adult), spanning the period before and after the onset of hearing (i.e., ~P11).…”

Section: Introductionmentioning

confidence: 99%

lncRNA expression in the auditory forebrain during postnatal development

Guo

Zhang

Sheng

et al. 2016

Gene

Self Cite

View full text Add to dashboard Cite

The biological processes governing brain development and maturation depend on complex patterns of gene and protein expression, which can be influenced by many factors. One of the most overlooked is the long noncoding class of RNAs (lncRNAs), which are known to play important regulatory roles in an array of biological processes. Little is known about the distribution of lncRNAs in the sensory systems of the brain, and how lncRNAs interact with other mechanisms to guide the development of these systems. In this study, we profiled lncRNA expression in the mouse auditory forebrain during postnatal development at time points before and after the onset of hearing (P7, P14, P21, adult). First, we generated lncRNA profiles of the primary auditory cortex (A1) and medial geniculate body (MG) at each age. Then, we determined the differential patterns of expression by brain region and age. These analyses revealed that the lncRNA expression profile was distinct between both brain regions and between each postnatal age, indicating spatial and temporal specificity during maturation of the auditory forebrain. Next, we explored potential interactions between functionally-related lncRNAs, protein coding RNAs (pcRNAs), and associated proteins. The maturational trajectories (P7 to adult) of many lncRNA – pcRNA pairs were highly correlated, and predictive analyses revealed that lncRNA-protein interactions tended to be strong. A user-friendly database was constructed to facilitate inspection of the expression levels and maturational trajectories for any lncRNA or pcRNA in the database. Overall, this study provides an in-depth summary of lncRNA expression in the developing auditory forebrain and a broad-based foundation for future exploration of lncRNA function during brain development.

show abstract

RNAseq by Total RNA Library Identifies Additional RNAs Compared to Poly(A) RNA Library

Cited by 42 publications

References 37 publications

Efficient and specific oligo-based depletion of rRNA

Efficient and specific oligo-based depletion of rRNA

Cross-Site Comparison of Ribosomal Depletion Kits for Illumina RNAseq Library Construction

lncRNA expression in the auditory forebrain during postnatal development

Contact Info

Product

Resources

About