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| Status |
Public on Jul 15, 2009 |
| Title |
Yeast-E. coli control, sonicated |
| Sample type |
SRA |
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| Source name |
yeast and E. coli
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| Organisms |
Escherichia coli; Saccharomyces cerevisiae |
| Characteristics |
strain: Yeast BY4730 (MAT a, leu2∆0, met15∆0, ura3∆0)
strain: E. coli JS5
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| 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. Fragments were purified by agarose gel electrophoresis. 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.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer |
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| Description |
n/a
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| 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.
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| Submission date |
Mar 11, 2009 |
| Last update date |
May 15, 2019 |
| Contact name |
Ghia Euskirchen |
| E-mail(s) |
ghia.euskirchen@stanford.edu
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| Organization name |
Stanford University
|
| Department |
Genetics
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| Lab |
Snyder
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| Street address |
1501 S. California Ave.
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| City |
Palo Alto |
| State/province |
CA |
| ZIP/Postal code |
94304 |
| Country |
USA |
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| Platform ID |
GPL10839 |
| Series (1) |
| GSE15188 |
Intrinsic histone-DNA interactions are not the major determinant of nucleosome positions in vivo |
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| Relations |
| SRA |
SRX012149 |
| BioSample |
SAMN00004272 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM379241_SONICATION_Ecoli_146bp.wig.gz |
1.6 Mb |
(ftp)(http) |
WIG |
| GSM379241_SONICATION_yeast_146bp.wig.gz |
2.4 Mb |
(ftp)(http) |
WIG |
| GSM379241_Sonicated_eland_result_laneA_FC14703_112307_s_2.txt.gz |
84.2 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Processed data provided as supplementary file |
| Raw data are available in SRA |
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