Buffer	Composition	Notes
Growth medium HEK293 cells	DMEM 10% FBS 2 mM L-glutamine 100 U/ml penicillin 100 U/ml streptomycin	Adjust growth conditions according to cell lines.
4-thiouridine (4SU) stock solution (1 M)	260.27 mg 4SU in 1 ml DMSO
Doxycycline stock solution (10 mg/ml)	10 mg doxycycline in 1 ml DMSO
PBS buffer	137 mM NaCl 2.7 mM KCl 10 mM Na2HPO4 1.8 mM KH2PO4
PBS-T buffer	PBS supplied with 0.1% Tween 20
1× NP40 lysis buffer	50 mM HEPES, pH 7.5 150 mM KCl 2 mM EDTA 1 mM NaF 2% (v/v) NP40 0.5 mM DTT complete EDTA-free Protease Inhibitor Cocktail (Roche) Phosphatase Inhibitor Cocktail tablets PhosSTOP (Roche)	Prepare a stock of 10× buffer without DTT and protease inhibitors. Add DTT and protease inhibitor directly before the experiment. One Protease Inhibitor Cocktail tablet for 50 ml buffer. One Phosphatase Inhibitor Cocktail tablet for 50 ml buffer.
IP-wash buffer	50 mM HEPES-KOH, pH 7.5 300 mM KCl 0.05% (v/v) NP40	Not every antibody will retain its binding ability in 300 mM KCl – adjust the salt concentration accordingly. If in doubt, use lysis buffer instead for washing.
High-salt wash buffer	50 mM HEPES-KOH, pH 7.5 500 mM KCl 0.05% (v/v) NP40	Not every antibody will retain its binding ability in 500 mM KCl – adjust the salt concentration accordingly. If in doubt, use lysis buffer instead for washing.
Dephosphorylation buffer	50 mM Tris-HCl, pH 7.9 100 mM NaCl 10 mM MgCl2 1 mM DTT	Composition is the same as 1× NEB buffer 3
Phosphatase wash buffer	50 mM Tris-HCl, pH 7.5 20 mM EGTA 0.5% (v/v) NP40
Polynucleotide kinase (PNK) buffer without DTT	50 mM Tris-HCl, pH 7.5 50 mM NaCl 10 mM MgCl2
PNK buffer	50 mM Tris-HCl, pH 7.5 50 mM NaCl 10 mM MgCl2 5 mM DTT	Composition is the same as 1× NEB PNK buffer
4× SDS PAGE loading buffer	10% glycerol (v/v) 50 mM Tris-HCl, pH 6.8 2 mM EDTA 2% SDS (w/v) 100 mM DTT 0.1% Bromophenol blue
10× SLAB 4 buffer	250 mM Tris-HCl, pH 8.5 1.9 M glycine 0.5% SDS
1× Transfer buffer	10% 10× SLAB 4 buffer 20% methanol 70% water
4× Proteinase K buffer	200 mM Tris-HCl, pH 7.5 300 mM NaCl 25 mM EDTA 4% (w/v) SDS
Acidic	25 ml acidic phenol
Phenol/chloroform/IAA	24 ml chloroform 1 ml isoamylalcohol
10× RNA ligase buffer without ATP	500 mM Tris-HCl, pH 7.6 100 mM MgCl2 100 mM 2-mercaptoethanol 1 mg/ml acetylated BSA (Sigma, B-8894)
10× RNA ligase buffer with ATP	500 mM Tris-HCl, pH 7.6 100 mM MgCl2 100 mM 2-mercaptoethanol 1 mg/ml acetylated BSA (Sigma, B-8894) 2 mM ATP
Denaturing PAA gel loading solution	98.8% formamide 1% (v/v) 0.5 M Na2 H2EDTA, pH 8.0 0.2% Bromophenol blue
10× dNTP solution	2 mM dATP 2 mM dCTP 2 mM dGTP 2 mM dTTP
10× PCR buffer	100 mM Tris-HCl pH 8.0 500 mM KCl 1% Triton-X-100 20 mM MgCl2 10 mM 2-mercaptoethanol