Single-tube linear DNA amplification (LinDA) for genome-wide studies using a few thousand cells
Pattabhiraman Shankaranarayanan, Marco-Antonio Mendoza-Parra, Wouter van Gool, Luisa M. Trindade and Hinrich Gronemeyer
Linear amplification of DNA (LinDA) by T7 polymerase is a versatile and robust method for generating sufficient amounts of DNA for genome-wide studies with minute amounts of cells (1,2). LinDA can be coupled to a great number of global profiling technologies. Indeed, chromatin immunoprecipitation combined with massive parallel sequencing (ChIP-seq) has been done for transcription factors and epigenetic modification of chromatin histones with 1,000 to 5,000 cells. LinDA largely simplified reChIP-seq experiments to monitor co-binding at chromatin target sites (3). The single tube design of LinDA is ideal for handling ultra-small amounts of DNA (<30pg) and is compatible with automation. The actual hands-on working time is less than 6h with one overnight reaction. A detailed LinDA protocol describing all materials and critical steps, in addition to examples and controls is available as part of the corresponding Nature Protocols publication (2).
TrimLinDA: a script for computational removal of polyA stretches
1 Single-tube linear DNA amplifi-
2 Single-tube linear DNA amplifi-
3. Sequential chromatin immunoprecipitation protocol for global analysis through massive parallel sequencing (reChIP-seq)