Working with Gel data
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What this section covers
This chapter focuses on the digital interpretation, annotation, and analysis of gel-based experimental data, including agarose gels, polyacrylamide gels (SDS-PAGE), and Western blots. It covers the key steps and tools for transforming gel images into meaningful, quantifiable results suitable for research reporting and publication.
What is gel data?
Gel data refers to the visual representation of molecular separation achieved through gel electrophoresis. The molecules can be DNA, RNA, or proteins, and the gel serves as a medium to separate them based on size, charge, or other properties.
This data is typically captured as digital images of gels. A gels can tells:
- whether a molecule is present or absent
- the size of the molecule using molecular weight or DNA ladders as references
- the relative abundance of the molecule
Agarose gel electrophoresis is used to separate DNA fragments by size. It is commonly to verify whether a PCR product is present.
SDS-PAGE using a polyacrylamide gel separates proteins based on size. By comparing to ladder of known sizes, the size of the proteins can be estimated. An SDS-PAGE will shows all the proteins in the sample.
Western blotting is used to identify specific proteins in an SDS-PAGE gel using antibodies. The proteins are transferred from the gel to a membrane, where they can be probed with antibodies that bind to the target protein.
What methods will we cover?
Importing gel images
Cropping, contrast adjustment, and rotation (without altering data integrity)
Manual and automated band detection
Measuring migration distances
Calculating Rf values and estimating molecular weights
Band intensity measurement
Annotation to label lanes, bands, and markers for publication