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Method: The use of exome capture RNA-seq for highly degraded RNA with application to clinical cancer sequencing
- Marcin Cieslik,
- Rashmi Chugh,
- Yi-Mi Wu,
- Ming Wu,
- Christine Brennan,
- Robert Lonigro,
- Fengyun Su,
- Rui Wang,
- Javed Siddiqui,
- Rohit Mehra,
- Xuhong Cao,
- David Lucas,
- Arul M. Chinnaiyan,
- and Dan Robinson
Genome Res. September 2015 25: 1372-1381; Published in Advance August 7, 2015, doi:10.1101/gr.189621.115
...construction of RNA-seq libraries. Genome Res 22: 134–141. Halvardson J, Zaghlool A, Feuk L. 2013. Exome RNA sequencing reveals rare and novel alternative transcripts. Nucleic Acids Res 41: e6. Harrow J, Frankish A, Gonzalez JM, Tapanari E, Diekhans M, Kokocinski F, Aken BL, Barrell D, Zadissa A, Searle S, et...
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Method: Systematic mapping of TF-mediated cell fate changes by a pooled induction coupled with scRNA-seq and multi-omics approaches
- Muyoung Lee,
- Qingqing Guo,
- Mijeong Kim,
- Joonhyuk Choi,
- Alia Segura,
- Alper Genceroglu,
- Lucy LeBlanc,
- Nereida Ramirez,
- Yu Jin Jang,
- Yeejin Jang,
- Bum-Kyu Lee,
- Edward M. Marcotte,
- and Jonghwan Kim
Genome Res. March 2024 34: 484-497; Published in Advance April 5, 2024, doi:10.1101/gr.277926.123
...-treated and control ES cells were dissociated into single cells with 0.25% trypsin-EDTA. The dissociated cells were washed twice with 0.04% BSA in PBS and resuspended to a concentration of 1000 cells per microliter. Then the cells were subjected to scRNA-seq. Single-cell libraries were generated using the chromium...
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Method: Tn5 transposase and tagmentation procedures for massively scaled sequencing projects
- Simone Picelli,
- Åsa K. Björklund,
- Björn Reinius,
- Sven Sagasser,
- Gösta Winberg,
- and Rickard Sandberg
Genome Res. December 2014 24: 2033-2040; Published in Advance July 30, 2014, doi:10.1101/gr.177881.114
...a reduction of the available volume in which the transposase can operate. Tagmentation of subpicogram amounts of cDNA In order to test the lower limit of input DNA required for tagmentation, we generated libraries from 500, 100, 10, 1, and 0.1 pg of double-stranded DNA. We successfully obtained RNA-seq...
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Method: In vitro, long-range sequence information for de novo genome assembly via transposase contiguity
- Andrew Adey,
- Jacob O. Kitzman,
- Joshua N. Burton,
- Riza Daza,
- Akash Kumar,
- Lena Christiansen,
- Mostafa Ronaghi,
- Sasan Amini,
- Kevin L. Gunderson,
- Frank J. Steemers,
- and Jay Shendure
Genome Res. December 2014 24: 2041-2049; Published in Advance October 19, 2014, doi:10.1101/gr.178319.114
...Spadden Gardener 2013; Shemesh et al. 2013; Wang et al. 2013). As such, there remains a strong need for robust in vitro methods to capture midrange contiguity information for de novo assembly. Transposase-mediated library construction, or ‘‘tagmentation,’’ utilizes a hyperactive Tn5 transposase to both fragment...
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Research: Transcriptomic landscape of transposable elements reveals LTR7-PLAAT4 as a potential oncogene and therapeutic target in pancreatic adenocarcinoma
- Meilong Shi,
- Chuanqi Teng,
- Shan Zhang,
- Xiaobo He,
- Lingyun Xu,
- Fengxian Han,
- Rongqi Wen,
- Ganjun Yu,
- Jingwen Liu,
- Yang Feng,
- Yanfeng Wu,
- Yan Ren,
- Gang Jin,
- and Jing Li
Genome Res. February 2026 36: 275-290; Published in Advance January 8, 2026, doi:10.1101/gr.280528.125
...PDAC cell lines, and hTERT-HPNE cell lines were retrieved from public repositories (see Supplemental Material).RNA-seq and DNA-seq library preparation and sequencingRNA-seq libraries were generated using the NEBNext Ultra RNA Library Prep kit for Illumina, followed by sequencing on the Illumina HiSeq X...
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Research: A gene regulatory element modulates myosin expression and controls cardiomyocyte response to stress
- Taylor Anglen,
- Irene M. Kaplow,
- Baekgyu Choi,
- Enya Dewars,
- Robin M. Perelli,
- Kevin T. Hagy,
- Duc Tran,
- Megan E. Ramaker,
- Svati H. Shah,
- Inkyung Jung,
- Andrew P. Landstrom,
- Ravi Karra,
- Yarui Diao,
- and Charles A. Gersbach
Genome Res. November 2025 35: 2418-2432; Published in Advance October 22, 2025, doi:10.1101/gr.280825.125
...for transposase-accessible chromatin using sequencing (ATAC-seq) and RNA sequencing (RNA-seq) on human induced pluripotent stem cell–derived cardiomyocytes (iPSC-CMs) to nominate cCREs (Corces et al. 2017). We then linked key regulatory elements to MYH6 and MYH7. We characterize the effects of epigenetic editing...
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Perspective: Tagmentation-based single-cell genomics
- Andrew C. Adey
Genome Res. October 2021 31: 1693-1705; doi:10.1101/gr.275223.121
...years since the initial description of transposase-based methods to prepare high-throughput sequencing libraries, or “tagmentation,” in which a hyperactive transposase is used to simultaneously fragment target DNA and append universal adapter sequences. Tagmentation effectively replaced a series...
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Method: Genome-wide CRISPR screening reveals genes essential for cell viability and resistance to abiotic and biotic stresses in Bombyx mori
- Jiasong Chang,
- Ruolin Wang,
- Kai Yu,
- Tong Zhang,
- Xiaoxu Chen,
- Yue Liu,
- Run Shi,
- Xiaogang Wang,
- Qingyou Xia,
- and Sanyuan Ma
Genome Res. May 2020 30: 757-767; Published in Advance May 18, 2020, doi:10.1101/gr.249045.119
...Bac transposase expression vector, A3-helper was from stocks stored in our laboratory. The CRISPR library delivery vector, pB-CRISPR, was constructed with the process described in the Supplemental Materials. The target vectors used to test the knockout efficiency of pB-CRISPR was constructed using library...
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Method: Ultra-low-input, tagmentation-based whole-genome bisulfite sequencing
- Andrew Adey and
- Jay Shendure
Genome Res. June 2012 22: 1139-1143; Published in Advance March 30, 2012, doi:10.1101/gr.136242.111
...: 779–785. Gertz J, Varley KE, Davis NS, Baas BJ, Goryshin IY, Vaidyanathan R, Kuersten S, Myers RM. 2012. Transposase mediated construction of RNA-seq libraries. Genome Res 22: 134–141. Grunenwald H, Baas B, Goryshin I, Zhang B, Adey A, Hu S, Shendure J, Caruccio N, Maffitt M. 2011. Nextera PCR...
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Method: RNA sequencing of Sleeping Beauty transposon-induced tumors detects transposon-RNA fusions in forward genetic cancer screens
- Nuri A. Temiz,
- Branden S. Moriarity,
- Natalie K. Wolf,
- Jesse D. Riordan,
- Adam J. Dupuy,
- David A. Largaespada,
- and Aaron L. Sarver
Genome Res. January 2016 26: 119-129; Published in Advance November 9, 2015, doi:10.1101/gr.188649.114
...Beauty ( SB )-mobilized T2/Onc transposons have been used to identify common insertion sites (CISs) associated with tumor formation. Recurrent sites of transposon insertion are commonly identified using ligation-mediated PCR (LM-PCR). Here, we use RNA sequencing (RNA-seq) data to directly identify...

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