Cenik et al. 2015 (PRJNA275386)
General Details
| Title | Integrative analysis of RNA, translation and protein levels reveals distinct regulatory variation across humans |
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| Organism | |
| Number of Samples | 50 |
| Release Date | 2015/02/13 00:00 |
| Sequencing Types | |
| Protocol Details |
Study Links
| GWIPS-viz | Trips-Viz |
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| Visit GWIPS-viz | Visit Trips-Viz |
Repository Details
| SRA | SRP055009 |
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| ENA | SRP055009 |
| GEO | GSE65912 |
| BioProject | PRJNA275386 |
Publication
| Title | |
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| Authors | Cenik C,Cenik ES,Byeon GW,Grubert F,Candille SI,Spacek D,Alsallakh B,Tilgner H,Araya CL,Tang H,Ricci E,Snyder MP |
| Journal | Genome research |
| Publication Date | 2015 Nov |
| Abstract | Elucidating the consequences of genetic differences between humans is essential for understanding phenotypic diversity and personalized medicine. Although variation in RNA levels, transcription factor binding, and chromatin have been explored, little is known about global variation in translation and its genetic determinants. We used ribosome profiling, RNA sequencing, and mass spectrometry to perform an integrated analysis in lymphoblastoid cell lines from a diverse group of individuals. We find significant differences in RNA, translation, and protein levels suggesting diverse mechanisms of personalized gene expression control. Combined analysis of RNA expression and ribosome occupancy improves the identification of individual protein level differences. Finally, we identify genetic differences that specifically modulate ribosome occupancy--many of these differences lie close to start codons and upstream ORFs. Our results reveal a new level of gene expression variation among humans and indicate that genetic variants can cause changes in protein levels through effects on translation. © 2015 Cenik et al.; Published by Cold Spring Harbor Laboratory Press. |
| PMC | PMC4617958 |
| PMID | 26297486 |
| DOI |
| Run Accession | Study Accession | Scientific Name | Cell Line | Library Type | Treatment | GWIPS-viz | Trips-Viz | Reads | BAM | BigWig (F) | BigWig (R) | ||
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| SRR1803146 | PRJNA275386 | Homo sapiens | lymphoblastoid | Ribo-Seq | Cycloheximide |  |
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| SRR1803147 | PRJNA275386 | Homo sapiens | lymphoblastoid | Ribo-Seq | Cycloheximide | |
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| SRR1803148 | PRJNA275386 | Homo sapiens | lymphoblastoid | Ribo-Seq | Cycloheximide | |
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| SRR1803149 | PRJNA275386 | Homo sapiens | lymphoblastoid | Ribo-Seq | Cycloheximide | |
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| SRR1803150 | PRJNA275386 | Homo sapiens | lymphoblastoid | Ribo-Seq | Cycloheximide | |
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| SRR1803151 | PRJNA275386 | Homo sapiens | lymphoblastoid | Ribo-Seq | Cycloheximide | |
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| SRR1803152 | PRJNA275386 | Homo sapiens | lymphoblastoid | Ribo-Seq | Cycloheximide | |
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| SRR1803153 | PRJNA275386 | Homo sapiens | lymphoblastoid | Ribo-Seq | Cycloheximide | |
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| SRR1803154 | PRJNA275386 | Homo sapiens | lymphoblastoid | Ribo-Seq | Cycloheximide | |
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| SRR1803155 | PRJNA275386 | Homo sapiens | lymphoblastoid | Ribo-Seq | Cycloheximide | |
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| SRR1803156 | PRJNA275386 | Homo sapiens | lymphoblastoid | Ribo-Seq | Cycloheximide | |
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| SRR1803157 | PRJNA275386 | Homo sapiens | lymphoblastoid | Ribo-Seq | Cycloheximide | |
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| SRR1803158 | PRJNA275386 | Homo sapiens | lymphoblastoid | Ribo-Seq | Cycloheximide | |
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| SRR1803159 | PRJNA275386 | Homo sapiens | lymphoblastoid | Ribo-Seq | Cycloheximide | |
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| SRR1803160 | PRJNA275386 | Homo sapiens | lymphoblastoid | Ribo-Seq | Cycloheximide | |
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| SRR1803161 | PRJNA275386 | Homo sapiens | lymphoblastoid | Ribo-Seq | Cycloheximide | |
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| SRR1803162 | PRJNA275386 | Homo sapiens | lymphoblastoid | Ribo-Seq | Cycloheximide | |
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| SRR1803163 | PRJNA275386 | Homo sapiens | lymphoblastoid | Ribo-Seq | Cycloheximide | |
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| SRR1803164 | PRJNA275386 | Homo sapiens | lymphoblastoid | Ribo-Seq | Cycloheximide | |
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| SRR1803165 | PRJNA275386 | Homo sapiens | lymphoblastoid | Ribo-Seq | Cycloheximide | |
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| SRR1803166 | PRJNA275386 | Homo sapiens | lymphoblastoid | Ribo-Seq | Cycloheximide | |
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| SRR1803167 | PRJNA275386 | Homo sapiens | lymphoblastoid | Ribo-Seq | Cycloheximide | |
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| SRR1803168 | PRJNA275386 | Homo sapiens | lymphoblastoid | Ribo-Seq | Cycloheximide | |
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| SRR1803169 | PRJNA275386 | Homo sapiens | lymphoblastoid | Ribo-Seq | Cycloheximide | |
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| SRR1803170 | PRJNA275386 | Homo sapiens | lymphoblastoid | Ribo-Seq | Cycloheximide | |
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| SRR1803171 | PRJNA275386 | Homo sapiens | lymphoblastoid | Ribo-Seq | Cycloheximide | |
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| SRR1803172 | PRJNA275386 | Homo sapiens | lymphoblastoid | Ribo-Seq | Cycloheximide | |
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| SRR1803173 | PRJNA275386 | Homo sapiens | lymphoblastoid | Ribo-Seq | Cycloheximide | |
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| SRR1803174 | PRJNA275386 | Homo sapiens | lymphoblastoid | Ribo-Seq | Cycloheximide | |
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| SRR1803175 | PRJNA275386 | Homo sapiens | lymphoblastoid | Ribo-Seq | Cycloheximide | |
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| SRR1803176 | PRJNA275386 | Homo sapiens | lymphoblastoid | Ribo-Seq | Cycloheximide | |
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| SRR1803177 | PRJNA275386 | Homo sapiens | lymphoblastoid | Ribo-Seq | Cycloheximide | |
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| SRR1803178 | PRJNA275386 | Homo sapiens | lymphoblastoid | Ribo-Seq | Cycloheximide | |
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| SRR1803179 | PRJNA275386 | Homo sapiens | lymphoblastoid | Ribo-Seq | Cycloheximide | |
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| SRR1803180 | PRJNA275386 | Homo sapiens | lymphoblastoid | Ribo-Seq | Cycloheximide | |
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| SRR1803181 | PRJNA275386 | Homo sapiens | lymphoblastoid | Ribo-Seq | Cycloheximide | |
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| SRR1803182 | PRJNA275386 | Homo sapiens | lymphoblastoid | Ribo-Seq | Cycloheximide | |
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| SRR1803183 | PRJNA275386 | Homo sapiens | lymphoblastoid | Ribo-Seq | Cycloheximide | |
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| SRR1803184 | PRJNA275386 | Homo sapiens | lymphoblastoid | Ribo-Seq | Cycloheximide | |
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| SRR1803185 | PRJNA275386 | Homo sapiens | lymphoblastoid | Ribo-Seq | Cycloheximide | |
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| SRR1803186 | PRJNA275386 | Homo sapiens | lymphoblastoid | Ribo-Seq | Cycloheximide | |
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| SRR1803187 | PRJNA275386 | Homo sapiens | lymphoblastoid | Ribo-Seq | Cycloheximide | |
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| SRR1803188 | PRJNA275386 | Homo sapiens | lymphoblastoid | Ribo-Seq | Cycloheximide | |
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| SRR1803189 | PRJNA275386 | Homo sapiens | lymphoblastoid | Ribo-Seq | Cycloheximide | |
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| SRR1803190 | PRJNA275386 | Homo sapiens | lymphoblastoid | Ribo-Seq | Cycloheximide | |
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| SRR1803191 | PRJNA275386 | Homo sapiens | lymphoblastoid | Ribo-Seq | Cycloheximide | |
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| SRR1803192 | PRJNA275386 | Homo sapiens | lymphoblastoid | Ribo-Seq | Cycloheximide | |
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| SRR1803193 | PRJNA275386 | Homo sapiens | lymphoblastoid | Ribo-Seq | Cycloheximide | |
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| SRR1803194 | PRJNA275386 | Homo sapiens | lymphoblastoid | Ribo-Seq | Cycloheximide | |
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| SRR1803195 | PRJNA275386 | Homo sapiens | lymphoblastoid | Ribo-Seq | Cycloheximide | |
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| Run Accession | Study Accession | Scientific Name | Cell Line | Library Type | Treatment | GWIPS-viz | Trips-Viz | Reads | BAM | BigWig (F) | BigWig (R) |
ⓘ For more Information on the columns shown here see: About