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Series GSE52809 Query DataSets for GSE52809
Status Public on Jan 29, 2014
Title Poly(A)-tail profiling reveals an embryonic switch in translational control
Organisms Arabidopsis thaliana; Schizosaccharomyces pombe; Saccharomyces cerevisiae; Drosophila melanogaster; Danio rerio; Xenopus laevis; Homo sapiens; Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary Poly(A) tails enhance the stability and translation of most eukaryotic messenger RNAs, but difficulties in globally measuring poly(A)-tail lengths have impeded greater understanding of poly(A)-tail function. Here we describe poly(A)-tail length profiling by sequencing (PAL-seq) and apply it to measure tail lengths of millions of individual RNAs isolated from yeasts, cell lines, Arabidopsis thaliana leaves, mouse liver, and zebrafish and frog embryos. Poly(A)-tail lengths were conserved between orthologous mRNAs, with mRNAs encoding ribosomal proteins and other 'housekeeping' proteins tending to have shorter tails. As expected, tail lengths were coupled to translational efficiencies in early zebrafish and frog embryos. However, this strong coupling diminished at gastrulation and was absent in non-embryonic samples, indicating a rapid developmental switch in the nature of translational control. This switch complements an earlier switch to zygotic transcriptional control and explains why the predominant effect of microRNA mediated deadenylation concurrently shifts from translational repression to mRNA destabilization.
Overall design 64 samples from a variety of species
Contributor(s) Subtelny AO, Eichhorn SW, Chen GR, Sive H, Bartel DP
Citation(s) 24476825
Submission date Nov 27, 2013
Last update date May 15, 2019
Contact name Stephen Eichhorn
Organization name Whitehead Institute for Biomedical Research
Department Biology
Lab Bartel
Street address 9 Cambridge Center
City Cambridge
State/province MA
ZIP/Postal code 02142
Country USA
Platforms (13)
GPL9061 Illumina Genome Analyzer II (Drosophila melanogaster)
GPL9115 Illumina Genome Analyzer II (Homo sapiens)
GPL9250 Illumina Genome Analyzer II (Mus musculus)
Samples (64)
GSM1276537 Pombe_RNA
GSM1276538 Pombe_RPF
GSM1276539 Liver_RNA
BioProject PRJNA230112
SRA SRP033369

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE52809_3T3.txt.gz 317.9 Kb (ftp)(http) TXT
GSE52809_3T3_contact_inhibited_1.txt.gz 201.2 Kb (ftp)(http) TXT
GSE52809_3T3_contact_inhibited_2.txt.gz 216.7 Kb (ftp)(http) TXT
GSE52809_3T3_polysome_profile_0_ribosomes.txt.gz 187.3 Kb (ftp)(http) TXT
GSE52809_3T3_polysome_profile_11_ribosomes.txt.gz 224.1 Kb (ftp)(http) TXT
GSE52809_3T3_polysome_profile_1_ribosome.txt.gz 199.0 Kb (ftp)(http) TXT
GSE52809_3T3_polysome_profile_2_ribosomes.txt.gz 216.0 Kb (ftp)(http) TXT
GSE52809_3T3_polysome_profile_3_ribosomes.txt.gz 211.3 Kb (ftp)(http) TXT
GSE52809_3T3_polysome_profile_4_ribosomes.txt.gz 193.6 Kb (ftp)(http) TXT
GSE52809_3T3_polysome_profile_5.5_ribosomes.txt.gz 217.0 Kb (ftp)(http) TXT
GSE52809_3T3_polysome_profile_7.5_ribosomes.txt.gz 219.3 Kb (ftp)(http) TXT
GSE52809_Arabidopsis.txt.gz 266.9 Kb (ftp)(http) TXT
GSE52809_Cerevisiae.txt.gz 139.4 Kb (ftp)(http) TXT
GSE52809_Cerevisiae_total.txt.gz 70.2 Kb (ftp)(http) TXT
GSE52809_Dre_132_2hpf.txt.gz 375.3 Kb (ftp)(http) TXT
GSE52809_Dre_132_4hpf.txt.gz 338.0 Kb (ftp)(http) TXT
GSE52809_Dre_132_6hpf.txt.gz 342.9 Kb (ftp)(http) TXT
GSE52809_Dre_155_2hpf.txt.gz 378.5 Kb (ftp)(http) TXT
GSE52809_Dre_155_4hpf.txt.gz 348.0 Kb (ftp)(http) TXT
GSE52809_Dre_155_6hpf.txt.gz 339.6 Kb (ftp)(http) TXT
GSE52809_Dre_mock_2hpf.txt.gz 334.8 Kb (ftp)(http) TXT
GSE52809_Dre_mock_4hpf.txt.gz 335.5 Kb (ftp)(http) TXT
GSE52809_Dre_mock_6hpf.txt.gz 329.9 Kb (ftp)(http) TXT
GSE52809_Drosophila.txt.gz 122.5 Kb (ftp)(http) TXT
GSE52809_HEK293T.txt.gz 340.9 Kb (ftp)(http) TXT
GSE52809_HeLa.txt.gz 281.9 Kb (ftp)(http) TXT
GSE52809_HeLa_total.txt.gz 276.1 Kb (ftp)(http) TXT
GSE52809_Liver.txt.gz 282.3 Kb (ftp)(http) TXT
GSE52809_Pombe.txt.gz 147.1 Kb (ftp)(http) TXT
GSE52809_RAW.tar 104.5 Gb (http)(custom) TAR (of TXT)
GSE52809_README.txt 2.2 Kb (ftp)(http) TXT
GSE52809_Xla_st12_12.5.txt.gz 286.9 Kb (ftp)(http) TXT
GSE52809_Xla_st3_4.txt.gz 286.8 Kb (ftp)(http) TXT
GSE52809_Xla_st9.txt.gz 290.2 Kb (ftp)(http) TXT
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Raw data are available in SRA
Processed data are available on Series record
Processed data provided as supplementary file

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