GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Series GSE68016 Query DataSets for GSE68016
Status Public on Jun 25, 2015
Title Mapping nucleosome resolution chromosome folding in yeast by Micro-C
Organism Saccharomyces cerevisiae
Experiment type Other
Summary We describe a Hi-C based method, Micro-C, in which micrococcal nuclease is used instead of restriction enzymes to fragment chromatin, enabling nucleosome resolution chromosome folding maps. Analysis of Micro-C maps for budding yeast reveals abundant self-associating domains similar to those reported in other species, but not previously observed in yeast. These structures, far shorted than topologically-associating domains in mammals, typically encompass one to five genes in yeast. Strong boundaries between self-associating domains occur at promoters of highly transcribed genes, and regions of rapid histone turnover that are typically bound by the RSC chromatin-remodeling complex. Investigation of chromosome folding in mutants confirms roles for RSC, “gene looping” factor Ssu72, Mediator, H3K56 acetyltransferase Rtt109, and N-terminal tail of H4 in folding of the yeast genome. This approach provides detailed structural maps of a eukaryotic genome and our findings provide insights into the machinery underlying chromosome compaction.
Overall design Chromatin is fragmented by Mnase, subsequenct nucleosomal end repair, and a modified two-step method for purfiying ligation products. Using Illumina paired-end sequencing maps Micro-C library and generates nucleosome resolution contact maps.

The readme.txt file contains additional description of how each processed data file was generated.
Contributor(s) Rando OJ, Hsieh TS
Citation(s) 26119342
Submission date Apr 17, 2015
Last update date May 15, 2019
Contact name Xavier Darzacq
Phone 510-642-0884
Organization name University of California, Berkeley
Department Molecular and Cell Biology
Lab Darzacq Lab
Street address 475D Li Ka Shing Center
City Berkeley
State/province CA
ZIP/Postal code 94720
Country USA
Platforms (2)
GPL13821 Illumina HiSeq 2000 (Saccharomyces cerevisiae)
GPL19756 Illumina NextSeq 500 (Saccharomyces cerevisiae)
Samples (91)
GSM1661107 BY4741_rep1
GSM1661108 BY4741_rep2
GSM1661109 BY4741_rep3-1
BioProject PRJNA281500
SRA SRP057391

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE68016_Boundary_calls_for_wild-type_yeast.xlsx 671.2 Kb (ftp)(http) XLSX
GSE68016_Gene_compaction_scores_for_all_datasets_with_multiple_replicates.xlsx 2.7 Mb (ftp)(http) XLSX
GSE68016_Gene_compaction_scores_for_temperature-sensitive_dataset.xlsx 1.2 Mb (ftp)(http) XLSX
GSE68016_Micro-C_interactions_vs._distance_for_MNase_titrations.xlsx 2.7 Mb (ftp)(http) XLSX
GSE68016_Micro-C_interactions_vs._distance_for_all_datasets.xlsx 11.9 Mb (ftp)(http) XLSX
GSE68016_NDR-spanning_reads_for_all_replicates.xlsx 2.8 Mb (ftp)(http) XLSX
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap