Genomics

Dataset Information

152

Transcriptome-wide measurement of ribosomal occupancy by ribosome profiling


ABSTRACT: Experiments for optimization of the ribosome profiling protocol using C. elegans lysates. We report that optimizing the cutting accuracy to a narrow window of 28-30 nucleotides when PAGE-purifying the ribosome-protected fragments (RPFs) significantly improves the quality of the RPF library. In addition, we find that purifying monosomes by sucrose gradient fractionation clearly removed more contaminating ribosomal RNA from the samples compared to the purification by gel filtration columns. Overall design: Experiment 1 (samples 1-4): Comparison between different methods to isolate monosomes and between different library preparations. Experiment 2 (samples 5-8): Optimization of the cutting accuracy to PAGE purify ribosome-protected fragments.

INSTRUMENT(S): Illumina HiSeq 2000 (Caenorhabditis elegans)

SUBMITTER: Jieyi Xiong 

PROVIDER: GSE65948 | GEO | 2018-02-12

REPOSITORIES: GEO

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Transcriptome-wide measurement of ribosomal occupancy by ribosome profiling.

Aeschimann Florian F   Xiong Jieyi J   Arnold Andreas A   Dieterich Christoph C   Großhans Helge H  

Methods (San Diego, Calif.) 20150620


Gene expression profiling provides a tool to analyze the internal states of cells or organisms, and their responses to perturbations. While global measurements of mRNA levels have thus been widely used for many years, it is only through the recent development of the ribosome profiling technique that an analogous examination of global mRNA translation programs has become possible. Ribosome profiling reveals which RNAs are being translated to what extent and where the translated open reading frame  ...[more]

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