|
| Status |
Public on Jan 24, 2011 |
| Title |
Cross-linking partial digestion |
| Sample type |
SRA |
| |
|
| Source name |
yeast culture, cross-linking, partial digestion
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
strain: JKM139
mnase digestion time: 5 min
growth temperature: 28C
treatment: formaldehyde cross-linking
|
| Treatment protocol |
For crosslinking chromatin prior to MNase digestion, cells were incubated with 1% formaldehyde for 15min and quenched with 0.125M glycine prior to cell harvesting.
|
| Growth protocol |
3ml pre-culture of Saccharomyces cerevisiae strain JKM139 in YE media was diluted to 500ml of YE media. For the optimal growth samples, the culture was grown to OD600= 0.7-0.8 at 28oC. For the heat-stressed samples, an ensuing step of 36oC incubation (water bath) for 20 minutes was applied.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
The cell pellet was subjected to zymolase treatment and MNase digestion. After MNase digestion, supernatant was collected by centrifugation and used as affinity purification material. DNA was extracted and subjected to electrophoresis. Mono-nucleosomal DNA bands (~150bp) were recovered and subjected to Illumina massive sequencing.
|
| |
|
| Library strategy |
MNase-Seq |
| Library source |
genomic |
| Library selection |
MNase |
| Instrument model |
Illumina Genome Analyzer |
| |
|
| Description |
CL.partial
DNA fragment size selection ~150 bp.
|
| Data processing |
Alignment: Sequence reads were obtained and mapped to the yeast (October, 2003; sacCer1) genome using the Illumina Genome Analyzer Pipeline. All reads mapping with two or fewer mismatches were retained.
|
| |
|
| Submission date |
Jan 03, 2011 |
| Last update date |
May 15, 2019 |
| Contact name |
Yuanxin Xi |
| E-mail(s) |
[email protected]
|
| Phone |
530-220-2067
|
| Organization name |
The University of Texas MD Anderson Cancer Center
|
| Department |
Bioinformatics and Computational Biology
|
| Street address |
1400 Pressler St
|
| City |
Houston |
| State/province |
TX |
| ZIP/Postal code |
77030 |
| Country |
USA |
| |
|
| Platform ID |
GPL9134 |
| Series (1) |
| GSE26412 |
MNase digestion-sensitive nucleosomes in Saccharomyces cerevisiae |
|
| Relations |
| SRA |
SRX037443 |
| BioSample |
SAMN00189634 |
