|
| Status |
Public on Sep 16, 2011 |
| Title |
chd1del_isw1del_MNase |
| Sample type |
SRA |
| |
|
| Source name |
Mnase digested chromatin
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
strain: TOH1358
library selection: gel purified mononucleosomes
|
| Growth protocol |
Liquid suspension cultures were inoculated from starter cultures and grown O/N in YPAD at 30C.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Yeast suspension cultures were grown in rich media (YPAD) at 30oC O/N to a cell density of 1-4 x107 nucleated cells/ml. Cells were cross-linked by addition of formaldehyde to a final concentration of 1% v/v for 10 minutes at room temperature (RT). Crosslinking was quenched with addition of 2.5 M glycine to a final concentration of 0.125 M and cells were further incubated for another 5 min at RT. Crosslinked cells were washed 3x with ice cold TBS (20mM Tris pH 7.5, 120 mM NaCl) and finally resuspended in 1M Sorbitol. Spheroplast preparation and micrococcal nuclease digestion of chromatin were carried out as previously described (3). Nucleosomal fragments were gel purified from 1.5% agarose gels run in TBE and DNA was extracted with QIAGEN gel extraction kits and subject to paired end sequencing using the Illumina platform
|
| |
|
| Library strategy |
MNase-Seq |
| Library source |
genomic |
| Library selection |
MNase |
| Instrument model |
Illumina Genome Analyzer |
| |
|
| Description |
processed data file build: sacCer1, Oct, 2003
mono-nucleosomes
|
| Data processing |
The average DNA length of paired-end samples is 150 bp +/- 40 bp.
Read sequences for each sample were received as two FASTQ files one for each fragment. These sequences were aligned to the Yeast SGD database (obtained from the SGD site as FASTA files dated Nov 2006) using Bowtie 0.12.3 as unique matched paired reads (5) as unique matched paired reads with maximum fragment length of 500bp to create a SAM file. A BAM file was created using samtools and once sorted was subsequently used to create a BED coverage file. The BAM file was then used to create a BigWig file.
|
| |
|
| Submission date |
Jul 28, 2011 |
| Last update date |
May 15, 2019 |
| Contact name |
Triantafyllos Gkikopoulos |
| E-mail(s) |
t.gkikopoulos@dundee.ac.uk
|
| Phone |
00441382345807
|
| Fax |
+441382388072
|
| Organization name |
University of Dundee
|
| Department |
College of Life Sciences
|
| Lab |
Tom Owen-Hughes
|
| Street address |
Dow Street
|
| City |
Dundee |
| State/province |
Angus |
| ZIP/Postal code |
DD1 5EH |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL9134 |
| Series (1) |
| GSE31015 |
A role for Snf2 related nucleosome spacing enzymes in genome-wide nucleosome organization |
|
| Relations |
| SRA |
SRX097122 |
| BioSample |
SAMN00717453 |
