Table S1.

Comparison of footprint preparation in Arabidopsis ribosome profiling

Experimental procedure	Liu et al., 2013 (25)	Juntawong et al., 2014 (26)	Merchante et al., 2015 (27)	Hsu et al., 2016 (current study)
Polysome extraction buffer	pH 8, medium ionic strength/buffering capacity	pH 9, high ionic strength/buffering capacity	∼pH 9, medium ionic strength/buffering capacity	pH 8, low ionic strength/buffering capacity
Amount of starting materials	Not specified	15-mL pulverized tissues	1.5 g	0.1 g
Pellet polysomes	Not required	Sucrose cushion (ultracentrifugation for 18 h)	Sucrose cushion (ultracentrifugation for 3.5 h)	Not required
RNase digestion condition	Directly digest with the polysome extracts in a large volume for 1 h	Pellet polysomes, resuspend in medium ionic strength/buffering capacity buffer, digest for 2 h	Pellet polysomes, resuspend in a large volume of medium ionic strength/buffering capacity buffer, digest for 2 h	Directly digest with the polysome extracts for 1 h
Monosome isolation	Sucrose cushion (ultracentrifugation, time not specified)	Sucrose gradient (ultracentrifugation for 1.5 h) and fractionation	Sucrose cushion (ultracentrifugation for 3.5 h), then sucrose gradient (ultracentrifugation 2.5 h) and fractionation	Size exclusion columns (benchtop centrifuge, 2 min)
Size of footprints isolated	Not specified	25–35 nt	28–32 nt	28–30 nt
Resulting % reads in the max reading frame for 28-nt footprints	∼58	∼37	∼62	92–96