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E-GEOD-65912 - Integrative analysis of RNA, translation and protein levels reveals distinct regulatory variation across humans

Status
Released on 14 February 2015, last updated on 3 April 2015
Organism
Homo sapiens
Samples (68)
Protocols (6)
Description
Elucidating the extent and 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 among humans. 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 levels, translation, and protein abundance 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. Ribosome profiling and RNA sequencing experiments from human lymphoblastoid cells
Experiment types
other, RNA-seq of coding RNA 
Contacts
Bilal Alsallakh, Can Cenik, Carlos L Araya, Damek Spacek, Elif Sarinay Cenik, Emiliano Ricci, Fabian Grubert, Gun W Byeon, Hagen Tilgner, Hua Tang, Jason A Reuter, Michael P Snyder, Sophie I Candille
MINSEQE
Exp. designProtocolsVariablesProcessedSeq. reads
Files
Investigation descriptionE-GEOD-65912.idf.txt
Sample and data relationshipE-GEOD-65912.sdrf.txt
Additional data (1)E-GEOD-65912.additional.1.zip
Links