Methods in Brief |
Featured
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Advertising Feature: Application Note |
Improved RNA-seq of blood-derived RNA increases gene discovery and coverage
RNA-seq of blood-derived RNA can aid discovery of the cause of disease, as well as preclinical research. However, the high content of globin mRNA and ribosomal RNA (rRNA) in blood samples limits the detection of rare transcripts and splice variants. The ScriptSeq™ Complete Kit (Blood) is a new method to prepare directional RNA-seq libraries that are virtually free of globin mRNA and rRNA contamination and exhibit high detection of reference and novel genes.
- Jim Pease
- & Cris Kinross
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Analysis |
Comparative analysis of RNA sequencing methods for degraded or low-input samples
This comparison of five RNA-seq library preparation methods highlights metrics for assessing the suitability of the methods for samples with low amounts of RNA and/or those with low-quality RNA.
- Xian Adiconis
- , Diego Borges-Rivera
- & Joshua Z Levin
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Research Highlights |
The genetic essence of our brains
A freely accessible transcriptional atlas offers unprecedented possibilities for exploring the human brain.
- Erika Pastrana
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Methods in Brief |
Single-cell transcriptome sequencing
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Methods in Brief |
The synaptic transcriptome
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Brief Communication |
Accurate identification of human Alu and non-Alu RNA editing sites
A computational framework is reported for the accurate and sensitive identification of RNA editing sites from whole-genome DNA and RNA sequences from the same individual.
- Gokul Ramaswami
- , Wei Lin
- & Jin Billy Li
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Methods in Brief |
Quantifying RNA localization
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Brief Communication |
A bioinformatics method identifies prominent off-targeted transcripts in RNAi screens
Reported is a method, genome-wide enrichment of seed sequence (GESS), to analyze primary data from siRNA screens to identify major off-targeted transcripts. Using GESS the authors identify off-targeted transcripts in several screens.
- Frederic D Sigoillot
- , Susan Lyman
- & Randall W King
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Brief Communication |
Combined RNAi and localization for functionally dissecting long noncoding RNAs
The systematic functional dissection of long non-coding RNA (lncRNA) is simplified using a combined knockdown and localization approach based on endoribonuclease-prepared siRNA (esiRNA). A pilot screen reveals lncRNAs involved in the maintenance of pluripotency.
- Debojyoti Chakraborty
- , Dennis Kappei
- & Frank Buchholz
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Methods in Brief |
In vivo detection of protein binding in the transcriptome
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Review Article |
Computational methods for transcriptome annotation and quantification using RNA-seq
- Manuel Garber
- , Manfred G Grabherr
- & Cole Trapnell
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Review Article |
Development and applications of single-cell transcriptome analysis
- Fuchou Tang
- , Kaiqin Lao
- & M Azim Surani
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Article |
FragSeq: transcriptome-wide RNA structure probing using high-throughput sequencing
High-throughput sequencing of RNA fragments generated from a single-strand RNA-specific nuclease followed by novel computational analysis yields structural insights into noncoding RNA at the transcriptome level.
- Jason G Underwood
- , Andrew V Uzilov
- & David Haussler
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Brief Communication |
De novo assembly and analysis of RNA-seq data
The Trans-ABySS pipeline is an integrated approach for transcript assembly and analysis to identify new mRNA isoforms and structures.
- Gordon Robertson
- , Jacqueline Schein
- & Inanc Birol
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Analysis |
Validation of two ribosomal RNA removal methods for microbial metatranscriptomics
Compared in this Analysis are two widely used procedures for ribosomal RNA removal in metatranscriptomic samples, and the authors present recommendations to prevent misleading analyses of microbial communities.
- Shaomei He
- , Omri Wurtzel
- & Philip Hugenholtz
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Article |
Linking promoters to functional transcripts in small samples with nanoCAGE and CAGEscan
Capturing the 5′ end of transcripts from an input of only 1,000 cells and linking the transcription start sites to downstream sequences allows the analysis of complex transcriptome architecture.
- Charles Plessy
- , Nicolas Bertin
- & Piero Carninci
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Article |
A paired-end sequencing strategy to map the complex landscape of transcription initiation
Paired-end reads consisting of 5′ transcription start sites and 3′ downstream sequences from transcripts in Drosophila melanogaster reveal distinct initiation patterns at different fly promoters and show that 5′ caps originating in coding regions are added posttranscriptionally.
- Ting Ni
- , David L Corcoran
- & Jun Zhu