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Research: Characteristics, origin, and potential for cancer diagnostics of ultrashort plasma cell-free DNA
- Irena Hudecova,
- Christopher G. Smith,
- Robert Hänsel-Hertsch,
- Chandra S. Chilamakuri,
- James A. Morris,
- Aadhitthya Vijayaraghavan,
- Katrin Heider,
- Dineika Chandrananda,
- Wendy N. Cooper,
- Davina Gale,
- Javier Garcia-Corbacho,
- Simon Pacey,
- Richard D. Baird,
- Nitzan Rosenfeld,
- and Florent Mouliere
Genome Res. February 2022 32: 215-227; Published in Advance December 20, 2021, doi:10.1101/gr.275691.121
...: In this window In a new window Figure 1. Differences in the recovery of ultrashort cfDNA fragments using different DNA extraction and DNA library preparation protocols. (A) Plasma samples from healthy individuals and cancer patients were processed by column (SC)-based and magnetic bead (MB)-based DNA extraction...
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Research: Historical RNA expression profiles from the extinct Tasmanian tiger
- Emilio Mármol-Sánchez,
- Bastian Fromm,
- Nikolay Oskolkov,
- Zoé Pochon,
- Panagiotis Kalogeropoulos,
- Eli Eriksson,
- Inna Biryukova,
- Vaishnovi Sekar,
- Erik Ersmark,
- Björn Andersson,
- Love Dalén,
- and Marc R. Friedländer
Genome Res. August 2023 33: 1299-1316; Published in Advance July 18, 2023, doi:10.1101/gr.277663.123
...alignments (de Filippo et al. 2018). Previous research (Smith et al. 2019) and our results show the usefulness of including ultrashort reads (18–30 nt) in obtaining comprehensive RNA abundance profiles. When mapping RNA reads to noncoding genes, the majority were assigned to rRNA genes (60% and 68...
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Method: Metabolic labeling of RNA using multiple ribonucleoside analogs enables the simultaneous evaluation of RNA synthesis and degradation rates
- Kentaro Kawata,
- Hiroyasu Wakida,
- Toshimichi Yamada,
- Kenzui Taniue,
- Han Han,
- Masahide Seki,
- Yutaka Suzuki,
- and Nobuyoshi Akimitsu
Genome Res. October 2020 30: 1481-1491; Published in Advance August 25, 2020, doi:10.1101/gr.264408.120
...of the estrogen response in MCF-7 breast cancer cells. RNA 22: 1592–1603. doi:10.1261/rna.056895.116 ↵Barrass JD, Reid JEA, Huang Y, Hector RD, Sanguinetti G, Beggs JD, Granneman S. 2015. Transcriptome-wide RNA processing kinetics revealed using extremely short 4tU labeling. Genome Biol 16: 282. doi:10.1186/s...
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Resource: Synthetic spike-in standards for RNA-seq experiments
- Lichun Jiang,
- Felix Schlesinger,
- Carrie A. Davis,
- Yu Zhang,
- Renhua Li,
- Marc Salit,
- Thomas R. Gingeras,
- and Brian Oliver
Genome Res. September 2011 21: 1543-1551; Published in Advance August 4, 2011, doi:10.1101/gr.121095.111
...; Morozova et al. 2009; Gerstein et al. 2010; Metzker 2010; Roy et al. 2010). RNA-seq offers single-nucleotide resolution, strand specificity, and short-range connectivity through pairedend sequencing. Because of these strengths, there has been great interest in using RNA-seq to distinguish isoforms...
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Method: A powerful and flexible statistical framework for testing hypotheses of allele-specific gene expression from RNA-seq data
- Daniel A. Skelly,
- Marnie Johansson,
- Jennifer Madeoy,
- Jon Wakefield,
- and Joshua M. Akey
Genome Res. October 2011 21: 1728-1737; Published in Advance August 26, 2011, doi:10.1101/gr.119784.110
...://www..org/cgi/doi/10.1101/gr.119784.110. 1728 Genome Research www..org 21:1728–1737 2011 by Cold Spring Harbor Laboratory Press; ISSN 1088-9051/11; www..org information present in RNA-seq data sets to reveal biological insights. Results ASE in the yeast We measured ASE by RNA-seq in a diploid hybrid of two diverse...
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Method: Nanopore-based consensus sequencing enables accurate multimodal tumor cell-free DNA profiling
- Li-Ting Chen,
- Myrthe Jager,
- Dàmi Rebergen,
- Geertruid J. Brink,
- Tom van den Ende,
- Willem Vanderlinden,
- Pauline Kolbeck,
- Marc Pagès-Gallego,
- Ymke van der Pol,
- Nicolle Besselink,
- Norbert Moldovan,
- Nizar Hami,
- Wigard P. Kloosterman,
- Hanneke van Laarhoven,
- Florent Mouliere,
- Ronald Zweemer,
- Jan Lipfert,
- Sarah Derks,
- Alessio Marcozzi,
- and Jeroen de Ridder
Genome Res. April 2025 35: 886-899; Published in Advance January 13, 2025, doi:10.1101/gr.279144.124
...BX, United Kingdom Corresponding authors: alessio.marcozzi@gmail.com, j.deridder-4@umcutrecht.nlAbstractShallow -wide cell-free DNA sequencing holds great promise for noninvasive cancer monitoring by providing reliable copy number alteration (CNA) and fragmentomic profiles. Single-nucleotide...
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Research: DDX54 regulates transcriptome dynamics during DNA damage response
- Miha Milek,
- Koshi Imami,
- Neelanjan Mukherjee,
- Francesca De Bortoli,
- Ulrike Zinnall,
- Orsalia Hazapis,
- Christian Trahan,
- Marlene Oeffinger,
- Florian Heyd,
- Uwe Ohler,
- Matthias Selbach,
- and Markus Landthaler
Genome Res. August 2017 27: 1344-1359; Published in Advance June 8, 2017, doi:10.1101/gr.218438.116
...lacking DDX54 binding (Fig. 4F). DDX54 is thus required for expression of its DDR-responsive target transcripts on both the mRNA and protein levels. DDX54 binding prevents intron retention and enhances pre-mRNA processing rate Because our findings revealed a binding preference of DDX54 toward weak 3...
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Resource: Tracking pre-mRNA maturation across subcellular compartments identifies developmental gene regulation through intron retention and nuclear anchoring
- Kyu-Hyeon Yeom,
- Zhicheng Pan,
- Chia-Ho Lin,
- Han Young Lim,
- Wen Xiao,
- Yi Xing,
- and Douglas L. Black
Genome Res. June 2021 31: 1106-1119; Published in Advance April 8, 2021, doi:10.1101/gr.273904.120
...maturation are important gene regulatory events that occur in distinct cellular locations. However, transcriptomic analyses often lose information on the subcellular distribution of processed and unprocessed transcripts. We generated extensive RNA-seq data sets to track mRNA maturation across subcellular...
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Research: RBFOX and PTBP1 proteins regulate the alternative splicing of micro-exons in human brain transcripts
- Yang I. Li,
- Luis Sanchez-Pulido,
- Wilfried Haerty,
- and Chris P. Ponting
Genome Res. January 2015 25: 1-13; Published in Advance December 18, 2014, doi:10.1101/gr.181990.114
...). The preferential positioning of nucleosomes within exons is hypothesized to aid exon recognition by slowing down RNA polymerase II, thereby allowing more time for the splicing machinery to assemble and splice out the intron immediately upstream (Schwartz et al. 2009).In contrast to ordinary exons, ultra-short...
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Resource: Efficient frequency-based de novo short-read clustering for error trimming in next-generation sequencing
- Wei Qu,
- Shin-ichi Hashimoto,
- and Shinichi Morishita
Genome Res. July 2009 19: 1309-1315; Published in Advance May 13, 2009, doi:10.1101/gr.089151.108
...18: 810–820. Chapman EJ, Carrington JC. 2007. Specialization and evolution of endogenous small RNA pathways. Nat Rev Genet 8: 884–896. Dohm JC, Lottaz C, Borodina T, Himmelbauer H. 2008. Substantial biases in ultra-short read data sets from high-throughput DNA sequencing. Nucleic Acids Res 36: e105...
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