|
| Status |
Public on Jun 18, 2012 |
| Title |
Nucleosomes_yeast_0.4mM_H2O2_40min |
| Sample type |
SRA |
| |
|
| Source name |
yeast
|
| Organism |
Saccharomyces cerevisiae S288C |
| Characteristics |
strain: BY4741
sequenced molecule: nucleosome-bound DNA
treatment: 0.4mM H2O2
time: 40 min
|
| Treatment protocol |
Yeast were treated with 0.4mM (final conc) H2O2 for varying amounts of time (range: 4-60 minutes)
|
| Growth protocol |
Yeast were grown at least 10 generations to an OD(600) ~0.6 in YPD medium at 30C.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were treated with formaldehyde (1%) for 15 minutes at 25C and quenched with 125mM glycine. Cells were digested to spheroplasts with zymolyase and treated with micrococcal nuclease for 20 minutes at 37C. DNA was purified as described in Liu et al (PLoS Biol, 2005). Libraries were generated using Illumina's "Preparing Samples for Paired End Sequencing" guide; size selection targeted 140-310bp fragments to capture mono- and di-nucleosomes. Clusters were generated using Cluster Kits (v2) and the Illumina Cluster Station with one sample per lane. A paired end, 75 bp run was performed using standard 36bp SBS kits (v3) and SCS 2.4 software. The majority of inserts will be about 150bp but there will be a population around 300bp as well.
|
| |
|
| Library strategy |
MNase-Seq |
| Library source |
genomic |
| Library selection |
MNase |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Description |
0.4mM H2O2 Timecourse in BY4741
The majority of inserts will be about 150bp but there will be a population around 300bp as well.
|
| Data processing |
Raw data were aligned to the yeast S288C. NC_001133.7 GI:144228165 build of the yeast genome using Bowtie allowing 1 mismatch across the length of the read (-v 1), removing any read that did not match uniquely to the genome (-m 1), using a minimum end-to-end distance of paired reads of 60bp (-I 60) and a maximum distance of 400bp (-X 400). Aligned reads were converted to sequence counts/bp across the genome using the compiler function of Maq. Nucleosome positions were called in each time point using the method of Kuan et al. Stat App Mol Bio Genet 8(1):Article 29
|
| |
|
| Submission date |
Jul 25, 2011 |
| Last update date |
May 15, 2019 |
| Contact name |
Dana J Huebert |
| Organization name |
University of Wisconsin-Madison
|
| Department |
Genetics
|
| Lab |
Audrey Gasch
|
| Street address |
425G Henry Mall
|
| City |
Madison |
| State/province |
WI |
| ZIP/Postal code |
53706 |
| Country |
USA |
| |
|
| Platform ID |
GPL13965 |
| Series (2) |
| GSE30900 |
Nucleosome occupancy dynamics in yeast BY4741 responding to 0.4mM H2O2 over time (0-60 min) |
| GSE30901 |
Dynamic changes to nucleosome occupancy and genomic expression in yeast responding to oxidative stress |
|
| Relations |
| SRA |
SRX092004 |
| BioSample |
SAMN00709502 |
