R-notebook-crispri-lib

A collection of data analysis notebooks for CRISPR interference libaries.

News

2023-09-22 | New CRISPRi library paper published in The Plant Cell

A new CRISPRi library for the cyanobacterium Synechocystis was previously constructed. This library has 5 guide RNAs targeting each gene. The characterization of the library and the results of our comprehensive fitness screening were now published in the The Plant Cell from Oxford University Press. The preprint is available on BioRxive.org. Briefly, the paper reveals trade-offs between growth rate and robustness against environmental changes. In other words, important genes in photosynthesis or carbon fixation/transport can be advantageous in many conditions but reduce fitness in others. This fitness cost can be attributed to the protein and energy cost for these non-utilized genes.

2022-05-06 | New Nextflow pipeline for CRISPRi library data

A new Nextflow-based pipeline for automated analysis of NGS CRISPRi library data is available, nf-core-crispriscreen. The pipeline is a much improved re-implementation of our old pipeline using all the great features from the nf-core community. Main advantages of nf-core/nextflow are automatic retrieval of latest software packages, containerization, native support of multi-core computation, and generally improved output of results.

2021-06-22 | Github repository moved

The original repository R-notebooks became too small and too diverse for all library projects. The CRISPRi library pipelines were therefore moved to this new dedicated repository, R-notebook-crispri-lib.

2021-05-01 | New CRISPRi library available

Based on the successful first CRISPRi library, a new Synechocystis sp PCC 6803 library with at least 5 sgRNAs instead of just 2 was designed and is currently tested. The library is available to researchers on request (michael.jahn@scilifelab.se, paul.hudson@scilifelab.se).

2021-02-08 | Pipeline for automatic CRISPRi lib data processing

A new pipeline for automated analysis of NGS data of PCR amplified sgRNAs is available on Github. The pipeline uses the popular DESeq2 package to estimate depletion and enrichment ('fitness') of sgRNA repression mutants.

2020-04-03 | CRISPRi library paper published

Our paper was published as Pooled CRISPRi screening of the cyanobacterium Synechocystis sp PCC 6803 for enhanced industrial phenotypes in Nature Communications! The preprint is available at BioRxiv.org.

Related publications

1. The second, new CRISPRi library in cyanobacteria with more sgRNAs per target is currently prepared for publication.
2. The first CRISPRi library in cyanobacteria was published in Yao et al., Nature Communications, 2020. The preprint is available at BioRxiv.org.

Overview

This repository contains data processing pipelines for the analysis of CRISPRi repression library data. The experiments were primarily carried out in the model cyanobacterium Synechocystis sp. PCC 6803. The repository contains raw data, processed data and R notebooks (*.Rmd) for:

• Next generation sequencing (NGS) of CRISPRi repression mutants
• NGS transcriptomics of knock-out mutants or wild type
• physiological measurements such as growth rate, cell pigmentation

All care was taken to guarantee scientific accuracy and adhere to good scientific practice in terms of statistics, reproducibility and code documentation. Please report any errors by filing a github issue for this repository, or contact michael.jahn@scilifelab.se.

Contents

• docs- rendered pipelines in html format
  • Synechocystis CRISPRi library data processing
  • Synechocystis CRISPRi library enrichment analysis
  • Synechocystis CRISPRi library additional tests
  • Synechocystis CRISPRi library V2 data processing
  • Synechocystis CRISPRi library V2 sgRNA features
• sgRNA_library - Synechocystis CRISPRi library Version 1 (Yao et al., 2020)
  • figures - exported figures from pipelines
  • pipeline - data processing pipelines, R markdown format (.Rmd)
  • processed_data - directory containing the output data
  • raw_data - directory containing the input
• sgRNA_library_V2 - Synechocystis CRISPRi library Version 2 (in preparation)
  • data - directory containing the input and output data
  • figures - exported figures from pipelines
  • pipeline - data processing pipelines, R markdown format (.Rmd)

How to run the pipelines

The pipelines collected in this repository are self-contained and executable. The code and the documentation are part of one and the same R markdown document for each pipeline. Pipelines can be downloaded and executed from the pipeline sub-folders. To simply view the rendered pipelines follow the links to the *.html reports at Contents.

To download the repository on your local drive use git clone in a (linux) terminal:

cd /your-target-folder
git clone https://github.com/m-jahn/R-notebook-crispri-lib.git

Open a pipeline with Rstudio and execute code (chunks) with the Run button. Alternatively, open an interactive R session and render the R markdown pipeline:

require(rmarkdown)
rmarkdown::render("pipeline.Rmd")