|
| Status |
Public on Jan 01, 2022 |
| Title |
∆ino80 MNase Replicate 2 |
| Sample type |
SRA |
| |
|
| Source name |
log cells
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
strain: deltaino80
genotype: MATa his3delta1 leu2delta0 met15delta0 ura3delta0 ino80::LEU2
|
| Treatment protocol |
Cells were fixed with 1% formaldehyde and quenched with 125mM glycine.
|
| Growth protocol |
Cells were grown to log phase in YPD.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were harvested spheroplasted with zymolyase, and chromatin was subjected to MNase digestion. The digested chromatin was treated with Proteinase K and the DNA was subsequently phenol chloroform extracted and ethanol precipitated. The samples were treated with RNaseA and hosphatase, then purified using a Qiagen PCR purification kit.
Libraries were prepared using the manufacturer's protocol for the Nugen Ovation Ultralow System V2 kit
|
| |
|
| Library strategy |
MNase-Seq |
| Library source |
genomic |
| Library selection |
MNase |
| Instrument model |
NextSeq 550 |
| |
|
| Description |
MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0 ino80::LEU2
|
| Data processing |
.fq files were aligned to reference .fa genome with bwa mem algorithm
.sam files were converted to .bam files and reads were sorted based on genome position using samtools 1.7
duplicate reads were removed using samtools
reads were indexed for python analysis
Supplementary_files_format_and_content: .bam, sorted, deduped, indexed reads (paired end)
|
| |
|
| Submission date |
Mar 11, 2021 |
| Last update date |
Jan 01, 2022 |
| Contact name |
Vijay Ramani |
| Organization name |
UCSF
|
| Department |
Biochemistry & Biophysics
|
| Lab |
Ramani Lab
|
| Street address |
600 16th St, GH-S312B
|
| City |
San Francisco |
| State/province |
California |
| ZIP/Postal code |
94143 |
| Country |
USA |
| |
|
| Platform ID |
GPL26302 |
| Series (1) |
| GSE168700 |
A hexasome is the preferred substrate for the INO80 chromatin remodeling complex allowing versatility of function |
|
| Relations |
| BioSample |
SAMN18256843 |
| SRA |
SRX10312995 |
