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Series GSE22571 Query DataSets for GSE22571
Status Public on Jun 25, 2010
Title Spliced leader trapping reveals widespread alternative splicing patterns in the highly dynamic transcriptome of Trypanosoma brucei
Organism Trypanosoma brucei
Experiment type Expression profiling by high throughput sequencing
Summary Some organisms like the human and animal parasite Trypanosoma brucei add a leader sequence to their mRNAs through a reaction called trans-splicing. Until now the splice sites for most mRNAs were unknown in T. brucei. Using high throughput sequencing we have developed a method to identify the splice sites and at the same time measure the abundance of the corresponding mRNAs. Analyzing three different life cycle stages of the parasite we identified the vast majority of splice sites in the organism and, to our great surprise, uncovered more than 2500 alternative splicing events, many of which appeared to be specific for one of the life cycle stages. Alternative splicing is a result of the addition of the leader sequence to different positions on the mRNA, leading to mixed mRNA populations that can encode for proteins with varying properties. One of the most obvious changes caused by alternative splicing is the gain or loss of targeting signals, leading to differential localization of the corresponding proteins. Based on our findings we hypothesize that alternative splicing is a major mechanism to regulate gene expression in T. brucei and could contribute to protein diversity in the parasite.
Overall design In total we sequenced three libraries from bloodstream form mRNA, (long slender and short stumpy, both Antat1.1 and monomorphic Lister 427), one from procyclic form mRNA (Antat1.1), 2x2 RNAi libraries (uninduced and induced), where each pair could be considered a biological replicate. Lastly we prepared and sequenced one conventional RNAseq library from procyclic mRNA (Antat1.1).
Contributor(s) Nilsson D, Gunasekera K, Mani J, Osteras M, Farinelli L, Baerlocher L, Roditi I, Ochsenreiter T
Citation(s) 20700444
Submission date Jun 25, 2010
Last update date May 15, 2019
Contact name Daniel Nilsson
Organization name University of Bern
Department Institute of Cell Biology
Street address Baltzerstrasse 4
City Bern
ZIP/Postal code 3012
Country Switzerland
Platforms (1)
GPL10599 Illumina Genome Analyzer II (Trypanosoma brucei)
Samples (9)
GSM560207 Tbrucei_Alba34_N_SLT (GDG-2)
GSM560208 Tbrucei_Alba34_I_SLT (GDG-3)
GSM560209 Tbrucei_BS_427_SLT (GDG-4)
SRA SRP002776
BioProject PRJNA128439

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Supplementary file Size Download File type/resource
GSE22571_RAW.tar 67.2 Mb (http)(custom) TAR (of TAR)
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data are available in SRA

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