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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Mar 03, 2016 |
| Title |
Wildtype mononucleosomes |
| Sample type |
SRA |
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| Source name |
log-phase liquid culture
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| Organism |
Schizosaccharomyces pombe |
| Characteristics |
strain: Hu0029
genotype: h- ura4D18 leu1-32 ade6-216
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Mononucleosomal DNA was prepared as described in Lantermann et al., Methods, 48(3), 218–225. doi:10.1016/j.ymeth.2009.02.004 .
NEBNext® ChIP-Seq Library Prep Master Mix Set for Illumina®
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| Library strategy |
MNase-Seq |
| Library source |
genomic |
| Library selection |
MNase |
| Instrument model |
Illumina MiSeq |
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| Data processing |
Alignment to the S. pombe genome was carried out using Bowtie2 with standard parameters for paired-end data.
Removal of clonal reads, read length adjustment, quantile normalization and calculation of differences in nucleosome occupancy were carried out with DANPOS (doi:10.1101/gr.142067.112)
Genome_build: Ensembl Genome Build ASM294v2.2, retrieved March 21, 2014, from http://www.pombase.org/downloads/datasets
Supplementary_files_format_and_content: Processed fixed step WIG files contain nucleosome occupancy scores (WT.wig and Fft2DFft3D.wig) and differential scores (+/- log10 of Poisson test p-values) as calculated by DANPOS with a step size of 10bp.
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| Submission date |
Apr 24, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Babett Steglich |
| Organization name |
Universitätsklinikum Hamburg-Eppendorf
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| Street address |
Martinistrasse 52
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| City |
Hamburg |
| ZIP/Postal code |
20246 |
| Country |
Germany |
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| Platform ID |
GPL16192 |
| Series (2) |
| GSE57067 |
Role of Fun30 remodelers in retrotransposon regulation [MNase-Seq] |
| GSE57069 |
Role of Fun30 remodelers in retrotransposon regulation |
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| Relations |
| Reanalyzed by |
GSM1399426 |
| BioSample |
SAMN02736992 |
| SRA |
SRX527205 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1374060_WT.wig.gz |
6.8 Mb |
(ftp)(http) |
WIG |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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