From: Charles <charles.plessy@oist.jp>
Date: Sat, 2 Nov 2019 03:28:40 +0000 (+0900)
Subject: FFPE-seq
X-Git-Url: https://source.charles.plessy.org/?a=commitdiff_plain;h=067bf2c10327e5270c3f287f5fb441f598aa1298;p=source.git

FFPE-seq
---

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
    Mg<sup>2+</sup> 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]]