Taguchi A, Nagasaka K, Plessy C, Nakamura H, Kawata Y, Kato S, Hashimoto K, Nagamatsu T, Oda K, Kukimoto I, Kawana K, Carninci P, Osuga Y, Fujii T.
Sci Rep. 2020 Oct 22;10(1):17991. doi:10.1038/s41598-020-75133-2
Use of Cap Analysis Gene Expression to detect human papillomavirus promoter activity patterns at different disease stages.
Poulain S, Arnaud O, Kato S, Chen I, Ishida H, Carninci P, Plessy C.
Nucleic Acids Res. 2020 Feb 6. pii: gkaa079. doi:10.1093/nar/gkaa079
Machine-driven parameter screen of biochemical reactions.
Our work using a Labcyte Echo machine to assemble thousands of nanoCAGE reactions.
Genome Res. 2019 Oct 24. doi:10.1101/gr.249656.119
Vahrenkamp JM, Szczotka K, Dodson MK, Jarboe EA, Soisson AP, Gertz J.
FFPEcap-seq: a method for sequencing capped RNAs in formalin-fixed paraffin-embedded samples.
Terminator, concatenation blocker, no manganese, indexes. Fails to cite our latest protocol.
Tan L, Lacko LA, Zhou T, Tomoiaga D, Hurtado R, Zhang T, Sevilla A, Zhong A, Mason CE, Noggle S, Evans T, Stuhlmann H, Schwartz RE, Chen S.
Nat Commun. 2019 Sep 13;10(1):4155. doi:10.1038/s41467-019-12063-2
Pre- and peri-implantation Zika virus infection impairs fetal development by targeting trophectoderm cells.
Poulain S, Kato S, Arnaud O, Morlighem JÉ, Suzuki M, Plessy C, Harbers M.
Methods Mol Biol. 2017;1543:57-109. doi:10.1007/978-1-4939-6716-2_4
NanoCAGE: A Method for the Analysis of Coding and Noncoding 5'-Capped Transcriptomes
BMC Genomics. 2015 Aug 13;16(1):597. doi:10.1186/s12864-015-1670-6
Cumbie JS, Ivanchenko MG, Megraw M.
NanoCAGE-XL and CapFilter: an approach to genome wide identification of high confidence transcription start sites.
Marques AC, Hughes J, Graham B, Kowalczyk MS, Higgs DR, Ponting CP
Genome Biol. 2013 Nov 29;14(11):R131
Chromatin signatures at transcriptional start sites separate two equally populated yet distinct classes of intergenic long noncoding RNAs.