|
| Status |
Public on Nov 25, 2013 |
| Title |
MN_Mei0h |
| Sample type |
SRA |
| |
|
| Source name |
Mononucleosomal DNA
|
| Organism |
Schizosaccharomyces pombe |
| Characteristics |
strain: h-/h- pat1.114/pat1.114 leu1.32/leu1.32 ade6M210/ade6M216
culture type: Synchronous meiosis
time: 0 hours
|
| Growth protocol |
For the Mei0h, Mei3h and Mei5h, cells were grown in Minimal Medium (MM) with 0,1 g/l leucine at 25 ºC (asynchronous) until OD595=0.8 followed by transfer to MM without nitrogen and 0,05 g/l leucine for 14 h after which NH4Cl was added to 0.5 g/l and leucine concentration was increased to 0,1 g/l. Samples were taken at 0h, 3h and 5h after transfer to 34 ºC to induce synchronous meiosis. For the Mit sample, cells were grown in rich medium (YES) at 32ºC until OD595=0.8. For the Mit_pat1.114, cells were grown in Minimal Medium (MM) with 0,1 g/l leucine at 25 ºC until OD595=0.8
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Chromatin was prepared from formaldehyde crosslinked log phase cells and digested with micrococcal nuclease (Fermentas #ENO181) to a final concentration of 180 units/ml for 40 minutes at 37 ºC to yield about 90% mononucleosomes. After reverting crosslink DNA of mononucleosomal size was purified from agarose gels.
Mononucleosomal DNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
MNase-Seq |
| Library source |
genomic |
| Library selection |
MNase |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Description |
Mononucleosomal DNA
|
| Data processing |
Alignment: bowtie 0.12.7
The smoothed signal generated by using the multilevel 1-D biorthogonal wavelet decomposition/reconstruction tool implemented in the Matlab “Wavelet Toolbox”, is used to calculate the average spacing between boundary peaks for individual nucleosomes.
The resulting combined profile was wavelet-smoothed to generate the final nucleosome positioning profile.
For all the genomic analyses, we have used as a reference the S. pombe genome version of 23/08/07 (http://www.pombase.org/ , ftp://ftp.sanger.ac.uk/pub/yeast/pombe/Chromosome_contigs/).
|
| |
|
| Submission date |
Oct 23, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Luis Quintales |
| Organization name |
Instituto de Biología Funcional y Genómica (IBFG)
|
| Department |
Universidad de Salamanca / CSIC
|
| Street address |
Calle Zacarías González, 2
|
| City |
Salamanca |
| ZIP/Postal code |
37007 |
| Country |
Spain |
| |
|
| Platform ID |
GPL15167 |
| Series (2) |
| GSE41772 |
Clustered regulatory signals at nucleosome-depleted regions punctuate a constant nucleosomal landscape in Schizosaccharomyces pombe [NGS_Illumina] |
| GSE41773 |
Clustered regulatory signals at nucleosome-depleted regions punctuate a constant nucleosomal landscape in Schizosaccharomyces pombe |
|
| Relations |
| SRA |
SRX200131 |
| BioSample |
SAMN01779504 |
