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Method: Simple and efficient profiling of transcription initiation and transcript levels with STRIPE-seq
- Robert A. Policastro,
- R. Taylor Raborn,
- Volker P. Brendel,
- and Gabriel E. Zentner
Genome Res. June 2020 30: 910-923; Published in Advance July 6, 2020, doi:10.1101/gr.261545.120
...methods in a conservative promoter window of −250 to +100 bp relative to the annotated start codons of 6572 mRNA transcripts. We observed good correlation between STRIPE-seq and SLIC-CAGE signal at promoters (Spearman's ρ = 0.708–0.743) (Fig. 4A). Although STRIPE-seq and nanoCAGE both rely on TSRT...
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Method: FFPEcap-seq: a method for sequencing capped RNAs in formalin-fixed paraffin-embedded samples
- Jeffery M. Vahrenkamp,
- Kathryn Szczotka,
- Mark K. Dodson,
- Elke A. Jarboe,
- Andrew P. Soisson,
- and Jason Gertz
Genome Res. November 2019 29: 1826-1835; Published in Advance October 24, 2019, doi:10.1101/gr.249656.119
..., Borkowska M, Müller F, Carninci P, Hajkova P, Lenhard B. 2018. SLIC-CAGE: high-resolution transcription start site mapping using nanogram-levels of total RNA. Genome Res 28: 1943–1956. doi:10.1101/gr.235937.118 ↵De Santa F, Barozzi I, Mietton F, Ghisletti S, Polletti S, Tusi BK, Muller H, Ragoussis J, Wei...
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