GSE112353
GSE GEO Potentially relatedActive ribosome profiling with RiboLace and standard ribosome profiling in HEK-293 cells
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Summary
We developed RiboLace, a novel method based on a new puromycin-containing molecule, for the isolation of active ribosomes by means of an antibody-free and tag-free pull-down approach. RiboLace is fast, it works with very low input material and can be easily and rapidly used to enhance Ribo-Seq, obtaining a global snapshot on active ribosome footprints at single nucleotide resolution from eukaryotic in vitro and in vivo systems. Keywords: ribosome profiling, translation, RiboLace, Ribo-Seq, active translation
Overall Design
We performed active ribosome profiling with RiboLace and standard ribosome profiling in HEK-293 cells. Experiments were performed in biological duplicate.
Analysis (5 steps)
View Data Processing- Raw reads were processed by removing 5â adapters, discarding reads shorter than 20 nucleotides and trimming the first nucleotide (using Trimmomatic v0.36).
- Reads mapping on rRNAs and tRNAs (downloaded from the SILVA rRNA and the Genomic tRNA databases respectively) were removed.
- The remaining reads were aligned to the human transcriptome (Ensembl v85, corresponding to GENCODE 25) with Bowtie2 (v2.2.6) employing the default settings.
- All reads aligning to the very same region were collapsed to avoid potential PCR duplicates, and only strand-specific reads were kept.
- The number of ribosome protected fragments was determined with samtools idxstats.
Supplementary Files (1)
GEO Samples (4)
Dataset Citations (1)
Potentially Related Publications (1)
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