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Deep-sequencing of degraded or cleaved RNAs from barley shoot and root growing in low-Pi condition.

ABSTRACT: Deep-sequencing of degraded or cleaved RNAs from barley shoot and root growing in low-Pi condition.

PROVIDER: PRJNA607200 | ENA |

REPOSITORIES: ENA

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Deep-sequencing of degraded or cleaved RNAs from barley shoot and root growing in low-Pi condition.

Project description:RNA was isolated from 23 old barley plants (shoots and roots), line Rolap. PARE libraries were constructed for both barley organs, followed by sequencing of NGS libraries.

2021-02-17 | GSE145423 | GEO

Barley shoot and root growing in low-Pi condition

Project description:This SuperSeries is composed of the SubSeries listed below.

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Barley shoot and root growing in low-Pi condition

Project description:Barley shoot and root growing in low-Pi condition

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Improved genome-wide mapping of uncapped and cleaved transcripts in eukaryotes—GMUCT 2.0

Project description:The advent of high-throughput sequencing has led to an explosion of studies into the diversity, expression, processing, and lifespan of RNAs. Recently, three different high-throughput sequencing-based methods have been developed to specifically study RNAs that are in the process of being degraded. All three methods—genome-wide mapping of uncapped and cleaved transcripts (GMUCT), parallel analysis of RNA ends (PARE), and degradome sequencing—take advantage of the fact that Illumina sequencing libraries use T4 RNA ligase 1 to ligate an adapter to the 5’ end of RNAs that have a free 5’-monophosphate. This condition for T4 RNA ligase 1 substrates means that mature mRNAs are not substrates of the enzyme because they have a 5’-cap. As a result, these sequencing libraries are specifically made up of clones of decapped or degrading mRNAs and the 3’ fragment of cleaved miRNA and siRNA targets. In this paper, we present a massively streamlined protocol for GMUCT that takes 2-3 days and can be initiated with as little as 5 µg of starting total RNA and involves only one gel size-selection step. We show that the results are similar to libraries made using the previous GMUCT protocol and PARE.

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