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RiboDoc: a Docker-based package for ribosome profiling analysis

ABSTRACT: RiboDoc: a Docker-based package for ribosome profiling analysis

PROVIDER: PRJNA727314 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR14421861.fastq.gz	Fastqsanger.gz
	SRR14421862.fastq.gz	Fastqsanger.gz
	SRR14421863.fastq.gz	Fastqsanger.gz
	SRR14421864.fastq.gz	Fastqsanger.gz

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RiboDoc: a Docker-based package for ribosome profiling analysis

Project description: Ribosome profiling (RiboSeq) has emerged as a powerful technique for studying the genome-wide regulation of translation in various cells. Several steps in the biological protocol have been improved, but the bioinformatics part of RiboSeq suffers from a lack of standardization, preventing the straightforward and complete reproduction of published results. Too many published studies provide insufficient detail about the bioinformatics pipeline used. The broad range of questions that can be asked with RiboSeq makes it difficult to use a single bioinformatics tool. Indeed, many scripts have been published for addressing diverse questions. Here, we propose a unique tool (for use with multiple operating systems, OS) to standardize the general steps that must be performed systematically in RiboSeq analysis, together with the statistical analysis and quality control of the sample. The data generated can then be exploited with more specific tools. We hope that this tool will help to standardize bioinformatics analyses pipelines in the field of translation.

2021-08-04 | GSE173856 | GEO

BacTRAP-based ribosome profiling of murine hypothalamic PNOC neurons

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Examples of ribosome profiling in chlamydomonas and mouse

Project description:Ribosome profiling is a technique that permits genome-wide, quantitative analysis of translation and has found broad application in recent years. Here, we describe a modified profiling protocol and software package designed to benefit more broadly the translation community in terms of simplicity and utility. The protocol, applicable to diverse organisms, including organelles, is based largely on previously published profiling methodologies, but employs duplex-specific nuclease as a convenient, bias-free, species-independent way to reduce rRNA contamination. Our protocol typically produces high levels of triplet periodicity, facilitating the detection of coding sequences, including upstream, downstream and overlapping open reading frames (ORFs). This feature also allows the identification of an alternative ribosome conformation evident during termination of protein synthesis. To test the effectiveness of DSN in ribosome profiling, we generated Ribo-Seq libraries from mouse tissue culture cells and from the green alga Chlamydomonas reinhardtii.

2015-10-16 | E-MTAB-2934 | biostudies-arrayexpress

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Ribosome profiling of HEK293 cells.

Project description:The development of the ribosome profiling (ribo-seq) technique has enabled the measurement of translation at a genome-wide level. There are several variants of the ribosome profiling technique that use different translation inhibitors. The regular ribo-seq utilizes Cycloheximide (CHX), a translation elongation inhibitor to freeze all translating ribosomes. In contrast to CHX, the translation inhibitor lactimidomycin (LTM) and harringtonine (Harr) have a much stronger effect on initiating ribosomes. The use of these inhibitors allows for the global mapping of translating initiating sites (TISs) when they are coupled with ribosome profiling (TI-seq). We have developed a computational tool to detect and/or quantitatively compare translation initiation from TI-seq data, and predict novel ORFs from regular CHX-based ribo-seq data. Two replicates of CHX-based ribo-seq experiments and one Harr based ribo-seq were performed in HEK293 cells for confirming the ORFs predicted using public available data.

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BacTRAP-based ribosome profiling of murine hypothalamic PNOC neurons

Project description:We performed a BacTRAP-based ribosome profiling of PNOC-expressing cells in the hypothalamus of mice. Therefore, we employed mice, which express a fusion protein of the ribosomal L10a protein with EGFP (L10a-EGFP) under control of the PNOC promoter (Doyle et al., 2008). Precipitation of ribosomes of hypothalamic PNOC neurons with anti-GFP antibodies and subsequent mRNA sequencing of associated mRNAs allowed for assessment of an in-depth translational profile of these cells. Affinity purification of translating ribosomes was performed as described by (Heiman et al., 2014) with minor modifications.

2020-04-16 | GSE137626 | GEO

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