Table 2.

Summary of datasets analyzed in this study, and corresponding figures using the datasets

DOI: http://dx.doi.org/10.7554/eLife.05005.022

Figure	Gene expression omnibus (GEO) ID, ArrayExpress ID, or data source	Reference
Figure 1A, Figure 1—figure supplement 4A	GSM854425, GSM854430, GSM854431, GSM854436, GSM854437, GSM854442, GSM854443	(Bazzini et al., 2012)
Figure 1B, Figure 6B	GSM1012118, GSM1012119, GSM1012120, GSM1012121, GSM1012122, GSM1012123	(Loeb et al., 2012)
Figure 1C, Figure 1—figure supplement 2A, Figure 6C,D	E-TABM-232	(Rodriguez et al., 2007)
Figure 1D,F	GSM1122217, GSM1122218, GSM1122219, GSM1122220, GSM1122221, GSM1122222, GSM1122223, GSM1122224, GSM1122225, GSM1122226	(Helwak et al., 2013)
Figure 1E, Figure 1—figure supplement 3A–D, Figure 6I,J	GSM538818, GSM538819, GSM538820, GSM538821	(Hafner et al., 2010)
Figure 1G	GSM156524, GSM156532, GSM210897, GSM210898, GSM210901, GSM210903, GSM210904, GSM210907, GSM210909, GSM210911, GSM210913, GSM37599, http://psilac.mdc-berlin.de/download/ (let7b_32h, miR-30_32h, miR-155_32h, miR-16_32h)	(Lim et al., 2005; Grimson et al., 2007; Linsley et al., 2007; Selbach et al., 2008)
Figure 1H, Figure 6K,L	E-MTAB-2110	(Tan et al., 2014)
Figure 1I, Figure 1—figure supplement 2B, Figure 6E	GSM1479572, GSM1479576, GSM1479580, GSM1479584	(Eichhorn et al., 2014)
Figure 1—figure supplement 1A	GSM210897, GSM210898, GSM210901, GSM210903, GSM210904, GSM210907, GSM210909, GSM210911, GSM210913, GSM37599, GSM37601	(Lim et al., 2005; Grimson et al., 2007)
Figure 1—figure supplement 1B, Figure 3, Figure 3—figure supplement 1B,C, Figure 4	74 datasets compiled in Supplementary data 4 of Garcia et al. (2011), used as is or after normalization (Supplementary file 1); GSM119707, GSM119708, GSM119710, GSM119743, GSM119745, GSM119746, GSM119747, GSM119749, GSM119750, GSM119759, GSM119761, GSM119762, GSM119763, GSM133685, GSM133689, GSM133699, GSM133700, GSM134325, GSM134327, GSM134466, GSM134480, GSM134483, GSM134485, GSM134511, GSM134512, GSM134551, GSM210897, GSM210898, GSM210901, GSM210903, GSM210904, GSM210907, GSM210909, GSM210911, GSM210913, GSM37599, GSM37601; E-MEXP-1402 (1595297366, 1595297383, 1595297389, 1595297394, 1595297399, 1595297422, 1595297427, 1595297432, 1595297491, 1595297496, 1595297501, 1595297507, 1595297513, 1595297518, 1595297524, 1595297530, 1595297535, 1595297564, 1595297588, 1595297595, 1595297605, 1595297614, 1595297621, 1595297627, 1595297644, 1595297650, 1595297662); E-MEXP-668 (16012097016666, 16012097016667, 16012097016668, 16012097016669, 16012097017938, 16012097017939, 16012097017952, 16012097017953, 16012097018568, 251209725411)	(Lim et al., 2005; Birmingham et al., 2006; Schwarz et al., 2006; Jackson et al., 2006a; Jackson et al., 2006b; Grimson et al., 2007; Anderson et al., 2008)
Figure 1—figure supplement 1C	GSM95614, GSM95615, GSM95616, GSM95617, GSM95618, GSM95619	(Giraldez et al., 2006)
Figure 1—figure supplement 1D,F	GSM1269344, GSM1269345, GSM1269348, GSM1269349, GSM1269350, GSM1269351, GSM1269354, GSM1269355, GSM1269356, GSM1269357, GSM1269360, GSM1269361, GSM1269362, GSM1269363	(Nam et al., 2014)
Figure 1—figure supplement 3E, Figure 6H	http://icb.med.cornell.edu/faculty/betel/lab/betelab_v1/Data.html	(Lipchina et al., 2011)
Figure 1—figure supplement 4B	http://psilac.mdc-berlin.de/media/database/release-1.0/protein/pSILAC_all_protein_ratios_OE.txt (miR155)	(Selbach et al., 2008)
Figure 3—figure supplement 1A	GSM416753	(Mayr and Bartel, 2009)
Figure 5, Figure 5—figure supplement 1	GSM156522, GSM156580, GSM156557, GSM156548, GSM156533, GSM156532, GSM156524, processed and normalized (Supplementary file 2)	(Linsley et al., 2007)
Figure 6A	GSM37601	(Lim et al., 2005)
Figure 6F,G	GSM363763, GSM363766, GSM363769, GSM363772, GSM363775, GSM363778	(Hausser et al., 2009)