Table 1: Ribosome profiling protocol conditions for the studies described in this work.

From: Comparative survey of the relative impact of mRNA features on local ribosome profiling read density

Table 1: Ribosome profiling protocol conditions for the studies described in this work.
DescriptionPMID (reference)SRA accessionBiological sourceLysis bufferLysis methodRNaseSeparationRNase digestion stage
    CHX pre-treatment, minsMg2+mMM+
mM
Drugs    
Human
 Andreev2562176427SRR1173909
SRR1173910
HEK293TNo1.5250 NaClCHXDetergentIGRLysate
 Cenik2629748628SRR1803149LCLNo5150 NaClCHXFreezeA,T1CSLysate
 Gonzalez2512289329SRR1562539BrainNo15250 NaClCHXDounce homogenizer, freezeIGRLysate
 Guo2070330030SRR057512HeLa85100 KClCHXDetergentIGRLysate
 Hsieh2236754131SRR403883PC3????????
 Lee2292742932SRR618771HEK293305100 KClCHXDetergentIGRPolysome
 Liu2329091656SRR619083HEK29335100 KClCHXDetergentIGRPolysome
 Loayzo-Puch2359452433SRR627620BJ fibroblast810100 KClCHXDetergentIGRLysate
 Rooijiers2430102035SRR935448BJ fibroblast510100 KClCHXDetergentIGRLysate
 Rubio2527384036SRR1573934MDA-MB-231No15220 NaClCHXDetergentICSLysate
 Shalgi2329091537SRR648667HEK293T55100 KClNoFreezeICSLysate
 Stadler CHX.2204522814SRR407637HeLaNo1.5140 KClCHXFreezeIGRLysate
 Stadleruntr.2204522814SRR407643HeLaNo1.5140 KClNoFreezeIGRLysate
 Stern-Ginossar, CHX2318085938SRR609197human foreskin fibroblasts115250 NaClCHXDetergentICSLysate
 Stern-Ginossar, untr2318085938SRR592961human foreskin fibroblastsNo15250 NaClNoDetergentICSLysate
 Stumpf2412066539SRR970561Hela25?CHXDetergentICSLysate
 
Mouse
 Howard2369664140SRR826795LiverNo10300 KClCHXHomogenizerICSLysate
 Ingolia, CHX220560417SRR315601Embryonic stem cell115250 NaClCHXDetergentICSLysate
 Ingolia, untr.220560417SRR315616Embryonic stem cellNo15250 NaClNoDetergentICSLysate
 Reid2521549241SRR1066893Embryonic fibroblastNo15100 KoAcCHXDetergent (digitonine)MNCSLysate
 Shalgi2329091537SRR6497523T355100 KClNoFreezeICSLysate
 Thoreen2255209842SRR449467Embryonic fibroblast57.5300 KClCHXDetergentIGRLysate
 
Yeast
 Artieri252942461SRR1049093 21.5140 KClCHXFreezeIGRLysate
 Brar2219441343SRR387871 21.5140 KClCHXFreezeIGRLysate
 Gardin253470646SRR1506632 NoARTseqARTseqCHXFreezeISCLysate
 Ingolia1921387744SRR014374
SRR014375
SRR014376
 21.5140 KClCHXFreezeIGRLysate
 Lareau, CHX248429908SRR1363415
SRR1363416
 Yes1.5140 KClCHXFreezeIGRLysate
 Lareau, untr.248429908SRR1363412
SRR1363413 SRR1363414
 No1.5140 KClNoFreezeIGRLysate
 McManus2431873045SRR948555 51.5140 KClCHXFreezeICSLysate
 Pop2553813912SRR1688547 21.5140 KClCHXFreezeICSLysate
  1. CHX, cycloheximide; CS, sucrose cushion; GR, sucrose gradient; MN, micrococcal nuclease; SC, spin-column chromotography. Additional information is provided in Supplementary Table 1. ?—not known.