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| Status |
Public on May 21, 2019 |
| Title |
An optimized FAIRE procedure for low cell numbers in yeast. |
| Organism |
Saccharomyces cerevisiae |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
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.
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| Overall design |
FAIRE assays of 8 samples: 4 FAIRE samples based on varying amounts of cells (4 mg, 20 mg, 100 mg and 500 mg) and 4 corresponding input DNA samples. 3 biological replicates per sample.
Please note that each processed narrowPeak file was generated from each sample pair (i.e. FAIRE and input, e.g. *F-R* and *I-R* samples) and is linked to the corresponding FAIRE sample record.
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| Contributor(s) |
Luque DS, Mizeranschi AE, Hlaváček O, Hughes T, Aaløkken R, Vachova L, Palkova Z, Gilfillan GD |
| Citation(s) |
29577419 |
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| Submission date |
Sep 22, 2017 |
| Last update date |
Jul 25, 2021 |
| Contact name |
Alexandru Mizeranschi |
| Organization name |
BIOCEV
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| Street address |
Průmyslová 595
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| City |
Vestec |
| ZIP/Postal code |
252 50 |
| Country |
Czech Republic |
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| Platforms (1) |
| GPL19756 |
Illumina NextSeq 500 (Saccharomyces cerevisiae) |
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| Samples (24)
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| Relations |
| BioProject |
PRJNA411771 |
| SRA |
SRP118588 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE104124_RAW.tar |
1.5 Mb |
(http)(custom) |
TAR (of NARROWPEAK) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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