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Literature DB >> 27798564

Single-cell sequencing of the small-RNA transcriptome.

Omid R Faridani¹, Ilgar Abdullayev^1,2, Michael Hagemann-Jensen^1,3, John P Schell^4,5, Fredrik Lanner^4,5, Rickard Sandberg^1,2.

Abstract

Little is known about the heterogeneity of small-RNA expression as small-RNA profiling has so far required large numbers of cells. Here we present a single-cell method for small-RNA sequencing and apply it to naive and primed human embryonic stem cells and cancer cells. Analysis of microRNAs and fragments of tRNAs and small nucleolar RNAs (snoRNAs) reveals the potential of microRNAs as markers for different cell types and states.

Entities: Disease Species

Mesh：

Substances：
MicroRNAs

Year: 2016 PMID： 27798564 DOI： 10.1038/nbt.3701

Source DB: PubMed Journal: Nat Biotechnol ISSN： 1087-0156 Impact factor: 54.908

23 in total

1. Counting absolute numbers of molecules using unique molecular identifiers.

Authors: Teemu Kivioja; Anna Vähärautio; Kasper Karlsson; Martin Bonke; Martin Enge; Sten Linnarsson; Jussi Taipale
Journal: Nat Methods Date: 2011-11-20 Impact factor: 28.547

Review 2. MicroRNAs in cancer: biomarkers, functions and therapy.

Authors: Josie Hayes; Pier Paolo Peruzzi; Sean Lawler
Journal: Trends Mol Med Date: 2014-07-12 Impact factor: 11.951

3. STAR: ultrafast universal RNA-seq aligner.

Authors: Alexander Dobin; Carrie A Davis; Felix Schlesinger; Jorg Drenkow; Chris Zaleski; Sonali Jha; Philippe Batut; Mark Chaisson; Thomas R Gingeras
Journal: Bioinformatics Date: 2012-10-25 Impact factor: 6.937

4. Entering the era of single-cell transcriptomics in biology and medicine.

Authors: Rickard Sandberg
Journal: Nat Methods Date: 2014-01 Impact factor: 28.547

5. Stress induces tRNA cleavage by angiogenin in mammalian cells.

Authors: Hanjiang Fu; Junjun Feng; Qin Liu; Fang Sun; Yi Tie; Jie Zhu; Ruiyun Xing; Zhixian Sun; Xiaofei Zheng
Journal: FEBS Lett Date: 2008-12-27 Impact factor: 4.124

6. tRNA cleavage is a conserved response to oxidative stress in eukaryotes.

Authors: Debrah M Thompson; Cheng Lu; Pamela J Green; Roy Parker
Journal: RNA Date: 2008-08-21 Impact factor: 4.942

7. A mammalian microRNA expression atlas based on small RNA library sequencing.

Authors: Pablo Landgraf; Mirabela Rusu; Robert Sheridan; Alain Sewer; Nicola Iovino; Alexei Aravin; Sébastien Pfeffer; Amanda Rice; Alice O Kamphorst; Markus Landthaler; Carolina Lin; Nicholas D Socci; Leandro Hermida; Valerio Fulci; Sabina Chiaretti; Robin Foà; Julia Schliwka; Uta Fuchs; Astrid Novosel; Roman-Ulrich Müller; Bernhard Schermer; Ute Bissels; Jason Inman; Quang Phan; Minchen Chien; David B Weir; Ruchi Choksi; Gabriella De Vita; Daniela Frezzetti; Hans-Ingo Trompeter; Veit Hornung; Grace Teng; Gunther Hartmann; Miklos Palkovits; Roberto Di Lauro; Peter Wernet; Giuseppe Macino; Charles E Rogler; James W Nagle; Jingyue Ju; F Nina Papavasiliou; Thomas Benzing; Peter Lichter; Wayne Tam; Michael J Brownstein; Andreas Bosio; Arndt Borkhardt; James J Russo; Chris Sander; Mihaela Zavolan; Thomas Tuschl
Journal: Cell Date: 2007-06-29 Impact factor: 41.582

8. Single-cell RNA-seq transcriptome analysis of linear and circular RNAs in mouse preimplantation embryos.

Authors: Xiaoying Fan; Xiannian Zhang; Xinglong Wu; Hongshan Guo; Yuqiong Hu; Fuchou Tang; Yanyi Huang
Journal: Genome Biol Date: 2015-07-23 Impact factor: 13.583

9. Bayesian approach to single-cell differential expression analysis.

Authors: Peter V Kharchenko; Lev Silberstein; David T Scadden
Journal: Nat Methods Date: 2014-05-18 Impact factor: 28.547

10. Systematic identification of culture conditions for induction and maintenance of naive human pluripotency.

Authors: Thorold W Theunissen; Benjamin E Powell; Haoyi Wang; Maya Mitalipova; Dina A Faddah; Jessica Reddy; Zi Peng Fan; Dorothea Maetzel; Kibibi Ganz; Linyu Shi; Tenzin Lungjangwa; Sumeth Imsoonthornruksa; Yonatan Stelzer; Sudharshan Rangarajan; Ana D'Alessio; Jianming Zhang; Qing Gao; Meelad M Dawlaty; Richard A Young; Nathanael S Gray; Rudolf Jaenisch
Journal: Cell Stem Cell Date: 2014-07-24 Impact factor: 24.633

66 in total

Single-cell sequencing of the small-RNA transcriptome.

1. Counting absolute numbers of molecules using unique molecular identifiers.

Review 2. MicroRNAs in cancer: biomarkers, functions and therapy.

3. STAR: ultrafast universal RNA-seq aligner.

4. Entering the era of single-cell transcriptomics in biology and medicine.

5. Stress induces tRNA cleavage by angiogenin in mammalian cells.

6. tRNA cleavage is a conserved response to oxidative stress in eukaryotes.

7. A mammalian microRNA expression atlas based on small RNA library sequencing.

8. Single-cell RNA-seq transcriptome analysis of linear and circular RNAs in mouse preimplantation embryos.

9. Bayesian approach to single-cell differential expression analysis.

10. Systematic identification of culture conditions for induction and maintenance of naive human pluripotency.

Review 1. The roles of microRNAs in mouse development.

2. Mapping specificity landscapes of RNA-protein interactions by high throughput sequencing.

3. Analysis of microRNA Regulation in Single Cells.

Review 4. Cross-species RNA-seq for deciphering host-microbe interactions.

Review 5. Chromatin loops and causality loops: the influence of RNA upon spatial nuclear architecture.

6. Two-tailed RT-qPCR: a novel method for highly accurate miRNA quantification.

7. MicroRNA Dynamics and Functions During Arabidopsis Embryogenesis.

Review 8. Unravelling biology and shifting paradigms in cancer with single-cell sequencing.

Review 9. Tumour heterogeneity and metastasis at single-cell resolution.

10. Angiogenin generates specific stress-induced tRNA halves and is not involved in tRF-3-mediated gene silencing.