paperKB
coga / coga-kb
Help
Sign in

Chunk #53 — Methods (full – for online materials) — RNA-seq samples and library preparation

Source
An atlas of active enhancers across human cell types and tissues.
Embedded
yes

Text

U of T4 RNA ligase 1 (New England Biolabs) and 1 μl of 10 mM ATP (New England Biolabs) at 20°C for 60 min. 4 μl of adapter ligated RNA was mixed with 1 μl of 20 μM RT Primer, 5’-CAA GCA GAA GAC GGC ATA CGA-3’, followed by incubation at 70°C for 2 min, and immediately kept on ice. RT reaction was done with 2 μl 5× Prime Script buffer, 1 μl of 10 mM dNTP, 20 U of RNaseOUT and 200 U of PrimeScript Reverse Transcriptase (TakaraBIO) at 44°C for 30 min. The cDNA product was amplified by PCR with 10 μl of 5× HF buffer, 1.25 μl of 10 mM each dNTP mix, 2 μl of 10 μM FWD primer, 5’-AAT GAT ACG GCG ACC ACC GAC AGG TTC AGA GTT CTA CAG TCC GA-3’, 2 μl of RT primer and 1 U of Phusion High-Fidelity DNA Polymerase (New England Biolabs). PCR was carried out in a total volume of 50 μl with the following thermal program; 98°C for 30 sec, 12 PCR cycles of 10 sec at 98°C, 30 sec at 60°C, and 15 sec at 72°C, followed by at 72°C for 5 min and then