|
| Status |
Public on Sep 20, 2016 |
| Title |
MN_Spombe_Figure2_WT_Rep1 |
| Sample type |
SRA |
| |
|
| Source name |
Mononucleosomal DNA
|
| Organism |
Schizosaccharomyces pombe |
| Characteristics |
strain: h- KanMX in IGR SPAC6F6.11c-SPAC6F6.12
|
| Growth protocol |
Yeast cultures were grown in YES medium (S. pombe) or YEPD (S. cerevisiae)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
In S. pombe maps: 200 ml cultures at 0.8x10^7 cells/ml were collected for preparation of mononucleosomal DNA. Cells were treated with 8 mg of Zymolyase 20T during 30 minutes at 30 ºC to induce spheroplasts formation. Mononucleosomal fragments were generated by digesting DNA with 150 units/ml of micrococcal nuclease (MNAse) at 37 ºC during 45 minutes. The amount of MNase was optimized experimentally to generate a 80:20 ratio of mononucleosomes to dinucleosomes, as described (Lantermann et al. 2010). Mononucleosomal DNA was recovered from 1.5% agarose gels and sequenced in an Illumina NextSeq 500 using the pair-end sequencing protocol.
In S. cerevisiae maps: 200 ml cultures at 0.8x10^7 cells/ml were collected for preparation of mononucleosomal DNA. Cells were treated with 10 mg of Zymolyase 20T during 5 minutes at 30 ºC to induce spheroplasts formation. Mononucleosomal fragments were generated by digesting DNA with 300 units/ml of micrococcal nuclease (MNAse) at 37 ºC during 10 minutes. The amount of MNase was optimized experimentally to generate a 80:20 ratio of mononucleosomes to dinucleosomes, as described (Soriano et al. 2014). Mononucleosomal DNA was recovered from 1.5% agarose gels and sequenced in an Illumina NextSeq 500 using the pair-end sequencing protocol.
Mononucleosomal DNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
MNase-Seq |
| Library source |
genomic |
| Library selection |
MNase |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Mononucleosomal DNA
|
| Data processing |
Alignment: bowtie 0.12.7. Aligment against the proper replaced with the appropriate sequence for each mutant.
The smoothed signal is generated by using a modified version of NUCwave to normalize signal against repetitions.
Genome_build: S. pombe 2007 (ASM294v2)
Genome_build: S. cerevisiae (SacCer 3)
|
| |
|
| Submission date |
Jul 27, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Enrique Vazquez de Luis |
| E-mail(s) |
quiquevzquez@gmail.com
|
| Organization name |
CNIC
|
| Lab |
Genomics Unit
|
| Street address |
Melchor Fernandez Almagro, 3
|
| City |
Madrid |
| State/province |
Madrid |
| ZIP/Postal code |
28029 |
| Country |
Spain |
| |
|
| Platform ID |
GPL20584 |
| Series (1) |
| GSE84910 |
Nucleosomal signatures impose nucleosome positioning in coding and non-coding sequences in the genome |
|
| Relations |
| BioSample |
SAMN05449360 |
| SRA |
SRX1980241 |
