From: Charles Date: Tue, 16 Feb 2021 03:59:28 +0000 (+0900) Subject: pubmed X-Git-Url: https://source.charles.plessy.org/?a=commitdiff_plain;h=a08b832d4f8d0f4cf56f758fe02e3ef80e37ab16;p=source%2F.git pubmed --- diff --git a/biblio/10.1101_2020.01.16.905182.mdwn b/biblio/10.1101_2020.01.16.905182.mdwn deleted file mode 100644 index a19df767..00000000 --- a/biblio/10.1101_2020.01.16.905182.mdwn +++ /dev/null @@ -1,10 +0,0 @@ -[[!meta title="Simple and efficient measurement of transcription initiation and transcript levels with STRIPE-seq"]] -[[!tag bioRxiv promoter method]] - -bioRxiv Posted January 16, 2020 doi:10.1101/2020.01.16.905182 - -Robert A. Policastro, R. Taylor Raborn, Volker P. Brendel and Gabriel E. Zentner - -Simple and efficient measurement of transcription initiation and transcript levels with STRIPE-seq - -[[!doi 10.1101/2020.01.16.905182 desc="Terminator-treated RNA reverse-transcribed with random N5 primers. The (biotinylated) TSO is added in the last 5 min of the RT (~40 µM final). The TSO carries a P5 linker and the RTP a P7 (indexed) linker. Follows a standard PCR and sequencing. The YR motif is detected in yeast and K562 cells. High amounts of rRNA remains in yeast"]] diff --git a/biblio/32660958.mdwn b/biblio/32660958.mdwn new file mode 100644 index 00000000..188300cf --- /dev/null +++ b/biblio/32660958.mdwn @@ -0,0 +1,10 @@ +[[!meta title="Simple and efficient measurement of transcription initiation and transcript levels with STRIPE-seq"]] +[[!tag promoter method]] + +Robert A. Policastro, R. Taylor Raborn, Volker P. Brendel and Gabriel E. Zentner + +Genome Res. 2020 Jun;30(6):910-923. doi:10.1101/gr.261545.120 + +Simple and efficient measurement of transcription initiation and transcript levels with STRIPE-seq + +[[!pmid 32660958 desc="Terminator-treated RNA reverse-transcribed with random N5 primers. The (biotinylated) TSO is added in the last 5 min of the RT (~40 µM final). The TSO carries a P5 linker and the RTP a P7 (indexed) linker. Follows a standard PCR and sequencing. The YR motif is detected in yeast and K562 cells. High amounts of rRNA remains in yeast"]] diff --git a/tags/template_switching.mdwn b/tags/template_switching.mdwn index 1d0d7a0b..35a15b58 100644 --- a/tags/template_switching.mdwn +++ b/tags/template_switching.mdwn @@ -55,6 +55,10 @@ ~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. + - [[Policastro and coll, 2020|bilbio/32660958]] and others before them add the + template-switching oligonucleotide after the reverse-transription has been + incubated for some time. + ### Effect of chemical composition of the TS oligonucleotide Originally, the TSOs were all-RNA. Since this is expensive to synthesise,