From: Charles Plessy Date: Thu, 19 Apr 2018 07:35:55 +0000 (+0900) Subject: STRT. X-Git-Url: https://source.charles.plessy.org/?a=commitdiff_plain;h=c3b0fb0fd85e414b2133163c01182a82e4f01a3e;p=source%2F.git STRT. --- diff --git a/biblio/21543516.mdwn b/biblio/21543516.mdwn new file mode 100644 index 00000000..8ead64b7 --- /dev/null +++ b/biblio/21543516.mdwn @@ -0,0 +1,10 @@ +[[!meta title="Characterization of the single-cell transcriptional landscape by highly multiplex RNA-seq."]] +[[!tag template_switching single_cell method transcriptome tags]] + +Islam S, Kjällquist U, Moliner A, Zajac P, Fan JB, Lönnerberg P, Linnarsson S. + +Genome Res. 2011 Jul;21(7):1160-7. doi:10.1101/gr.110882.110 + +Characterization of the single-cell transcriptional landscape by highly multiplex RNA-seq. + +[[!pmid 21543516 desc="Single-cell Tagged Reverse Transcription (STRT)"]] diff --git a/tags/template_switching.mdwn b/tags/template_switching.mdwn index 4619e756..edae7dbf 100644 --- a/tags/template_switching.mdwn +++ b/tags/template_switching.mdwn @@ -13,6 +13,10 @@ and `TTT` were also tested. An extensive protocol was published in [[Ginsberg, 2005|biblio/16308152]]. + - In the single-cell tagged reverse transcription (STRT) method, + [[Islam et al, 2011|biblio/21543516]]) use template switching and unique + molecular identifiers to sequence 5′ ends. The method is oligo-dT-primed. + - [[Mohr et al (2013)|biblio/23697550]] have shown (Fig 6) that retroviral RTs can extend a linker with the sequence of a small RNA via a template switching reaction. (That is: a sRNA can play the same role as a TS oligonucleotide.) @@ -34,6 +38,11 @@ as a replacement for RNA. - [[Arguel et al (2017)|biblio/27940562]] reported similar performance for RRR and RRL, using a 5′-focused method similar to nanoCAGE or STRT. +### Effect of TSO concentration + + - For the STRT method, [[Zajac et al (2013)|biblio/24392002]] concluded that + 1 μM of TSO gave the highest yield. + ### Effect of magnesium, manganese and dNTP concentrations - [[Schmidt and Mueller, 1999|biblio/10518626]] showed that increasing