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An optimized FAIRE procedure for low cell numbers in yeast.

ABSTRACT: We report an optimised low-input FAIRE-seq (Formaldehyde-Assisted Isolation of Regulatory Elements) procedure to assay chromatin accessibility from yeast colonies. Sensitivity, specificity and reproducibility of the scaled-down method are comparable to that of regular, higher input amounts, assayed over a 100-fold range. The method enables epigenetic analysis of chromatin structure to be assayed without the need for liquid culture, thus opening the possibility to study wild yeasts that form colonies, or those can be isolated in sufficient amounts in situ, from environmental samples.

ORGANISM(S): Saccharomyces cerevisiae

PROVIDER: GSE104124 | GEO | 2019/05/21

REPOSITORIES: GEO

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An optimized FAIRE procedure for low cell numbers in yeast.

Project description:We report an optimized low-input FAIRE-seq (Formaldehyde-Assisted Isolation of Regulatory Elements-sequencing) procedure to assay chromatin accessibility from limited amounts of yeast cells. We demonstrate that the method performs well on as little as 4 mg of cells scraped directly from a few colonies. Sensitivity, specificity and reproducibility of the scaled-down method are comparable with those of regular, higher input amounts, and allow the use of 100-fold fewer cells than existing procedures. The method enables epigenetic analysis of chromatin structure without the need for cell multiplication of exponentially growing cells in liquid culture, thus opening the possibility of studying colony cell subpopulations, or those that can be isolated directly from environmental samples.

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Limitations and possibilities of low cell number ChIP-seq

Project description:ChIP-seq experiments using low numbers of input cells, scaled down to the point where data quality is unnacceptably compromised, reveals limits of the technique. Two-part ChIPseq study using native chromatin (non-crosslinked) generated with MNase from human CD4+ cells. Part 1: Previously published protocol (Barski et al, 2007, Cell 129:823, hereafter called "Benchmark") used with 2x10e7 cells / ChIP with H3K4me3 antibody, compared to modified method ("new") with decreasing input cell numbers spanning 1000-fold range from 2x10e7 cells / IP to 2x10e4 cells/ IP. Part 2: reproducibility of new method studied using triplicate samples at lowest two cell numbers tested: 1x10e5 and 2x10e4 / ChIP, using H3K4me3 and H3K27me3 antisera.

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Project description:ChIP-seq experiments using low numbers of input cells, scaled down to the point where data quality is unnacceptably compromised, reveals limits of the technique.

2012-12-03 | GSE42147 | GEO

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