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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