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Sample GSM379240 Query DataSets for GSM379240
Status Public on Jul 15, 2009
Title Nucleosomes assembled on yeast and E. coli DNA by ACF
Sample type SRA
Source name yeast and E. coli
Organisms Escherichia coli; Saccharomyces cerevisiae
Characteristics strain: Yeast BY4730 (MAT a, leu2∆0, met15∆0, ura3∆0)
strain: E. coli JS5
Extracted molecule genomic DNA
Extraction protocol Yeast DNA was prepared from exponentially growing cells that were treated with Zymolyase. The resulting spherophasts were resuspended in Qiagen buffer G2 with 200μg/ml RNase A and then incubated with Proteinase K (8mg, Qiagen) for 30 minutes at 50C. After removal of cellular debris by centrifugation, DNA was precipitated with ethanol, isolated by spooling, and further purified using a Qiagen Genomic-tip 500/G according to the manufacturer’s instructions. E. coli DNA was isolated using a Qiagen Genomic-tip 500/G according to the manufacturer's instructions. Purified genomic DNA preparations from Saccharomyces cerevisiae as well as from Escherichia coli were sonicated separately to yield fragments that ranged in length from 5 to 10 kb. The resulting yeast and E. coli DNA samples were combined in a 3:1 mass ratio, and assembled into chromatin using a purified system containing recombinant Drosophila NAP-1 and ACF as well as purified native histones from Drosophila embryos. Chromatin was extensively digested with micrococcal nuclease to yield core particles. The ~147 bp DNA fragments derived from the core particles were purified by agarose gel electrophoresis. Mononucleosomal DNA was treated with calf intestinal alkaline phosphatase (New England Biolabs) to remove 3’ phosphate groups left after the micrococcal nuclease treatment. Libraries were prepared according to Illumina’s instructions accompanying the DNA Sample Kit (Part# 0801-0303) and sequenced on the Genome Analyzer following the manufacturer’s protocols.
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina Genome Analyzer
Description n/a
Data processing Sequence tags were obtained and aligned to the Saccharomyces cerevisiae from SGD2 (Apr 2008 build) and Escherichia coli K12 MG1655 (U00096) genomes using the Illumina/Solexa Analysis Pipeline. The analysis allowed 2 mismatches per mapped read and only uniquely aligned reads were retained. In sample 1 (Nucleosomes assembled on yeast and E. coli DNA by salt dialysis) and sample 2 (Nucleosomes assembled on yeast and E. coli DNA by ACF), each sequencing tag represents one end of a mono-nucleosomal DNA fragment. Therefore, we extended each tag to 146 bp in the 3’ direction to represent a whole mono-nucleosome, and then we piled up all extended sequencing tags in a sample to obtain the nucleosome density profile along the genome. The identical approach was also used in sample 3 (Yeast-Ecoli control, sonicated) to serve as control.
Submission date Mar 11, 2009
Last update date May 15, 2019
Contact name Ghia Euskirchen
Organization name Stanford University
Department Genetics
Lab Snyder
Street address 1501 S. California Ave.
City Palo Alto
State/province CA
ZIP/Postal code 94304
Country USA
Platform ID GPL10839
Series (1)
GSE15188 Intrinsic histone-DNA interactions are not the major determinant of nucleosome positions in vivo
SRA SRX012148
BioSample SAMN00004271

Supplementary file Size Download File type/resource
GSM379240_ACF_Ecoli_146bp.wig.gz 1.5 Mb (ftp)(http) WIG
GSM379240_ACF_eland_result_laneA_FC12187_102707_s_3.txt.gz 149.6 Mb (ftp)(http) TXT
GSM379240_ACF_eland_result_laneB_FC200RR_20080220_s_1.txt.gz 199.9 Mb (ftp)(http) TXT
GSM379240_ACF_yeast_146bp.wig.gz 4.6 Mb (ftp)(http) WIG
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data are available in SRA

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