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Table 1 Dataset summary

From: Estimation of ribosome profiling performance and reproducibility at various levels of resolution

Organism Dataset Condition Treatment Replicate Type Accession
C. elegans Stadler_2011 [26] L1 post CHX rep1
rep2
biological SRR405089
SRR405091-2
  Stadler_2012 [44] L1 post CHX rep1
rep2
rep3
rep4
biological SRR522871
SRR522872
SRR522896
SRR522897
D. rerio Bazzini_2012 [14] WT, 2hpf
WT, 6hpf
pre/post CHX rep1
rep2
rep1
rep2
biological SRR392998-9
SRR393000-1
SRR393006-7
SRR393008-9
E. coli Li_2012 [36] MOPS post GMPPNP+ Chloramphenicol rep1
rep2
biological SRR407274-5
SRR407276-7
  Oh_2011 [23] DSP pre/post Chloramphenicol rapid filtration rep1
rep2
rep3
biological SRR364364
SRR364366
SRR364368
H. sapiens Stadler_2011 [26] HeLa, CHX post CHX rep1
rep2
technical SRR407637
SRR407638
  Lee_2012 [54] HEK293T, CHX pre/post CHX rep1
rep2
technical SRR618770
SRR618771
  Liu_2013 [45] HeLa-tTA, K71M pre/post CHX rep1
rep2
biological SRR619099
SRR619100
  Stumpf_2013 [50] HeLa, G1 pre/post CHX rep1
rep2
biological SRR970490
SRR970538
  Andreev_2015 [48] HEK293T, control post CHX rep1
rep2
biological SRR1173905
SRR1173909-10
M. musculus Inoglia_2011 [38] mESC, noLIF-36 h
mESC, yesLIF
pre/post CHX rep1
rep2
rep1
rep2
rep3
biological SRR315620-2
SRR315623
SRR315601-2
SRR315624-6
SRR315627
S. cerevisiae Ingolia_2009 [10] YPD pre/post CHX rep1
rep2
biological SRR014374-6
SRR014377-81
  Brar_2012 [12] meiotic pre/post CHX rep1
rep2
biological SRR387904
SRR387905
  Artieri_2014 [43] YPD, mixed \w S. paradoxus pre/post CHX rep1
rep2
biological SRR1040415
SRR1040423, SRR1040427
  McManus_2014 [49] YPD pre/post CHX rep1
rep2
biological SRR948553
SRR948555
  1. Details for all analyzed datasets are provided. The Treatment column denotes which drug was used to arrest translation and whether it was added pre- and/or post-lysis