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Series GSE36063 Query DataSets for GSE36063
Status Public on May 17, 2012
Title A map of nucleosome positions in yeast at base-pair resolution
Organism Saccharomyces cerevisiae
Experiment type Other
Summary The exact positions of nucleosomes along genomic DNA can influence many aspects of chromosome function, yet existing methods for mapping nucleosomes do not provide the necessary single base pair accuracy to determine these positions. Here we develop and apply a new approach for direct mapping of nucleosome centers based on chemical modification of engineered histones. The resulting map locates nucleosome center positions genome-wide in unprecedented detail and accuracy. It reveals novel aspects of the in vivo nucleosome organization that are linked to transcription factor binding, RNA polymerase pausing, and the higher order structure of the chromatin fiber itself.
 
Overall design 6 samples were analyzed with high throughout parallel sequencing. All samples were created using the same chemical mapping protocol except with varying reaction times. The different reaction times did not make any significant difference in the nucleosome maps so all the data, for the 6 samples, were combined into one data set for the paper and are all considered replicates. The 6 samples are as follows: 1. 20 minute reaction time (single-end sequencing) 2. 20 minute reaction time (single-end sequencing) 3. 1 minute reaction time (single-end sequencing) 4. 1.5 minute reaction time (single-end sequencing) 5. 20 minute reaction time (paired-end sequencing) 6. 1.5 minute reaction time (paired-end sequencing)
 
Contributor(s) Brogaard KR, Xi L, Wang J, Widom J
Citation(s) 22722846
Submission date Feb 24, 2012
Last update date May 15, 2019
Contact name Ji-Ping Wang
E-mail(s) jzwang@northwestern.edu
Organization name Northwestern University
Street address 2006 Sheridan Road
City Evanston
ZIP/Postal code 60208
Country USA
 
Platforms (1)
GPL15263 AB SOLiD 4 System (Saccharomyces cerevisiae)
Samples (6)
GSM880646 20 min (single end) -1
GSM880647 20 min (single end) -2
GSM880648 1 min (single end)
Relations
SRA SRP011325
BioProject PRJNA151815

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
GSE36063_RAW.tar 5.4 Gb (http)(custom) TAR (of TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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