Ubiquitously transcribed genes use alternative polyadenylation to achieve tissue-specific expression
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...…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…...
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...…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,…...
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...…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…...
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...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) DOI: 10.7554/eLife.05005.022 Agarwal et al. eLife 2015;4:e05005....
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...In addition, many nonconserved interactions also function to reduce mRNA levels and protein output (Farh et al., 2005; Krutzfeldt et al., 2005; Lim et al., 2005; Baek et al., 2008; Selbach et al., 2008)....
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...Da Ribosomal protein families (158) Db mRBP families (422) Dc tRNA-binding protein families (130) 2....
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...Bartel DP. 2004....
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"Ubiquitously transcribed genes use ..." refers background in this paper
...On the other hand, nine out of 12 miRNAs whose target sites are enriched in the distal 39 UTRs of pAM genes are considered to be widely expressed (Supplemental Table 10; Wienholds et al. 2005; Landgraf et al. 2007)....
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