Assmann Lab presents

Orzya CLIMtools

Created by Ángel Ferrero-Serrano and Sally Assmann

Please cite: Ferrero-Serrano Á, Chakravorty D, Kirven KJ, Assmann SM. 2024
Oryza CLIMtools: A genome–environment association resource reveals adaptive roles for heterotrimeric G proteins in the regulation of rice agronomic traits,
Plant Communications, PMID: 38213027, https://doi.org/10.1016/j.xplc.2024.100813.

 

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Arabidopsis CLIMtools

Created by Ángel Ferrero-Serrano and Sally Assmann

Please cite: Ferrero-Serrano Á, Assmann SM. 2019
Phenotypic and genome-wide association with the local environment of Arabidopsis.
Nature Ecology and Evolution PMID:30643246, doi: 10.1038/s41559-018-0754-5

CLIMtools

 

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Protocols

Some of the protocols we use are available from the links below.

• Rice CRISPR protocol

• Preparation of Epidermal Peels and Guard Cell Protoplasts

• pDOE BiFC Vectors

• Biolistic Transformation of Guard Cells

• Gas Exchange

• Plant Electrophysiology

 

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Software

StructureFold2 is our signature bioinformatic tool to analyze in vivo RNA- structuromes using chemically probed RNA libraries. It is currently hosted on GitHub and frequently updated. Included on GitHub is an easy to follow manual.

StructureFold2 Dependencies

• cutadapt – read adapter and quality trimmer.
• Bowtie2 – Fast and sensitive read alignment.
• SAMtools – tools for working with the SAM/BAM format.
• RNAstructure package – folds RNA with constraints
• Vienna Package – folds RNA without constraints

We highly reccomend learning and using Python for most common bioinformatic tasks, as it is a versitile, easy to learn scripting language, with a fully developed host of resources.

We highly reccomend learning and using R for all statistical needs, as well as chart and graph generation. R has an almost endless variety of packages, custom-tailored for almost any sort of analysis.

 

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Scientific Links

Arabidopsis Information Portal (Araport)

• Araport Homepage

The Arabidopsis Information Resource (TAIR)

• TAIR homepage
• TAIR Arabidopsis BLAST homepage

Nottingham Arabidopsis Stock Centre (uNASC)

• uNASC homepage
• Growing Arabidopsis protocol
• Crossing Arabidopsis protocol

The Salk Institute Genomic Analysis Laboratory

• The Salk Institute Homepage
• SIGnal “T-DNA Express” Arabidopsis Gene Mapping
• SIGnal iSECT toolbox

National Center for Biotechnology Information Site

• NCBI Site Map
• NCBI PubMed homepage
• NCBI BLAST homepage

Online Analytical Tool link pages

• Biological Information Resource (U. of Washington)
• ABIM Online Analysis Tools (Université Aix-Mairseille)
• MEME Motif Scan

Other

• AGRICOLA, USDA National Agricultural Library
• How to think like a computer scientist – Start learning Python here!