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| Status |
Public on Dec 09, 2011 |
| Title |
Saccharomyces_cerevisiae-nucleosome-reads |
| Sample type |
SRA |
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| Source name |
Saccharomyces cerevisiae
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| Organism |
Saccharomyces cerevisiae |
| Characteristics |
strain: BY4741
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| Treatment protocol |
Cells were then cross-linked with formaldehyde and mono-nucleosomes were isolated according to modified protocols from Lee, Tillo., et al. Nature Genetics (2007)
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| Growth protocol |
Cells were grown in YPD (2% peptone, 1% yeast extract, 2% dextrose) starting from a overnight culture until they reached mid-log phase (0.8 OD).
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Mono-nucleosomes were extracted by treating the cell spheroplast with Mnase. Samples representing mono-nucleosomes were gel extracted, end repaired and adapter ligated.
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| Library strategy |
MNase-Seq |
| Library source |
genomic |
| Library selection |
MNase |
| Instrument model |
Illumina Genome Analyzer II |
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| Data processing |
The genome sequences were retrieved using SGD or Genolevures. Reads were mapped using Novocraft and only unique reads were further processed. As reads covered both ends of the ~150bp length DNA fragments that correspond to mono-nucleosomes, we converted the mapped positions into the estimated center position by adding or removing (depending on the strand) half the length of a typical DNA fragment. This typical length was evaluated in each sample by the distances between consecutive peaks of reads from the forward and backward strands, and was between 110bp to 130bp in all samples. For S. bayanus and C.glabrata, the reads from two biological repeats were combined into a single dataset. Data represents one-to-one orthologs which were defined based on Cliften et al. (Cliften, Sudarsanam et al. 2003) and Wapinski et al. (Wapinski, Pfeffer et al. 2007). Occupancy patterns were taken from -600 to +1000 (relative to the ATG) and for genes shorter than 1kb, we examined the pattern only until the end of the gene.
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| Submission date |
Aug 11, 2010 |
| Last update date |
May 15, 2019 |
| Contact name |
Kyle Tsui |
| E-mail(s) |
kyletsui@hotmail.com
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| Organization name |
University of Toronto
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| Lab |
HipHop
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| Street address |
160 College Street
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| City |
Toronto |
| ZIP/Postal code |
M5S 3E1 |
| Country |
Canada |
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| Platform ID |
GPL9377 |
| Series (1) |
| GSE23577 |
Nucleosome positioning for 4 yeast species |
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| Relations |
| SRA |
SRX025556 |
| BioSample |
SAMN00102769 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM578362_Scerevisiae.txt.gz |
4.2 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Processed data provided as supplementary file |
| Raw data are available in SRA |
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