From: Charles Date: Wed, 12 Dec 2018 04:28:49 +0000 (+0900) Subject: Café X-Git-Url: https://source.charles.plessy.org/?a=commitdiff_plain;h=5d0d135e738a41979d9a4d2d0527509defae84e0;p=source.git Café --- diff --git a/biblio/30355603.mdwn b/biblio/30355603.mdwn new file mode 100644 index 00000000..63258776 --- /dev/null +++ b/biblio/30355603.mdwn @@ -0,0 +1,10 @@ +[[!meta title="NanoPARE: parallel analysis of RNA 5' ends from low-input RNA."]] +[[!tag RNA-seq sequence_tags method library template_switching software]] + +Genome Res. 2018 Dec;28(12):1931-1942. doi:10.1101/gr.239202.118 + +Schon MA, Kellner MJ, Plotnikova A, Hofmann F, Nodine MD. + +NanoPARE: parallel analysis of RNA 5' ends from low-input RNA. + +[[!pmid 30355603 desc="5′ ends tags and RNA-seq tags separately amplified in two libraries."]] diff --git a/tags/template_switching.mdwn b/tags/template_switching.mdwn index b78625de..5226ecef 100644 --- a/tags/template_switching.mdwn +++ b/tags/template_switching.mdwn @@ -27,6 +27,12 @@ circulating RNAs, to remove phosphates or cyclophosphates that would prevent the A-tailing. + - in _nanoPARE_ ([[Schon, Kellner and coll.|biblio/30355603]]), a template-switching + oligonucleotide (RNA-RNA-LNA, without UMIs) is used to add a linker on 5′ ends. + After tagmentation, two libraries are amplified: one for 5′ ends and one for RNA-seq. + ~15% of the 5′ end alignments have extra Gs, but the genomic distribution is + bimodal. Peaks with significant amounts of "extra G" nucleotides are marked as TSS. + ### Effect of chemical composition of the TS oligonucleotide Originally, the TSOs were all-RNA. Since this is expensive to synthesise,