From 067bf2c10327e5270c3f287f5fb441f598aa1298 Mon Sep 17 00:00:00 2001 From: Charles Date: Sat, 2 Nov 2019 12:28:40 +0900 Subject: [PATCH] FFPE-seq --- biblio/31649055.mdwn | 10 ++++++++++ tags/manganese.mdwn | 6 ++++-- tags/template_switching.mdwn | 8 ++++++-- 3 files changed, 20 insertions(+), 4 deletions(-) create mode 100644 biblio/31649055.mdwn diff --git a/biblio/31649055.mdwn b/biblio/31649055.mdwn new file mode 100644 index 00000000..23854b46 --- /dev/null +++ b/biblio/31649055.mdwn @@ -0,0 +1,10 @@ +[[!meta title="FFPEcap-seq: a method for sequencing capped RNAs in formalin-fixed paraffin-embedded samples."]] +[[!tag nanoCAGE method template_switching manganese]] + +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. + +[[!pmid 31649055 desc="Terminator, concatenation blocker, no manganese, indexes. Fails to cite our latest protocol."]] diff --git a/tags/manganese.mdwn b/tags/manganese.mdwn index 5aec4360..7b7ff5a9 100644 --- a/tags/manganese.mdwn +++ b/tags/manganese.mdwn @@ -1,4 +1,6 @@ [[!meta title="pages tagged manganese"]] -[[!inline pages="tagged(manganese)" actions="no" archive="yes" -feedshow=10]] +See [[template_switching]] for the effect of manganese addition on cap +specificity of transcriptome methods. + +[[!inline pages="tagged(manganese)" limit=0]] diff --git a/tags/template_switching.mdwn b/tags/template_switching.mdwn index ece27413..351d4908 100644 --- a/tags/template_switching.mdwn +++ b/tags/template_switching.mdwn @@ -57,7 +57,8 @@ as a replacement for RNA. - 5′ iso-dC and iso-dG prevents reverse-transcriptase to reach the end of the TSO, and therefore blocks concatenation - ([[Kapteyn et al., 2010|biblio/20598146]]). + ([[Kapteyn et al., 2010|biblio/20598146]]). This was also used in + FFPEcap-seq ([[Vahrenkamp and coll., 2019|biblio/31649055]]). ### Effect of TSO concentration @@ -73,9 +74,12 @@ as a replacement for RNA. concentration: 1 mM each. [[Pinto & Lindblad (2010)|biblio/19837043]] also used manganese. - - [[Lee et al (2017)|biblio/28327113]] increased the efficiency of template + - [[Lee and coll. (2017)|biblio/28327113]] increased the efficiency of template switching non-capped molecules by increasing dNTPs to 2 mM and Mg2+ to 9 mM. + - [[Vahrenkamp and coll. (2019)|biblio/31649055]] reported that addition of + 1 mM manganese increases the formation of TSO concatenates and the fraction + of reads aliging to ribosomal sequences. [[!inline pages="tagged(template_switching)" limit=0]] -- 2.47.3