|
| Status |
Public on Jul 16, 2018 |
| Title |
h1D-h2D_Sen1-AID+Aux_Rad52ChIP-seq_2 |
| Sample type |
SRA |
| |
|
| Source name |
yeast
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
strain/background: 288C
genotype/variation: h1D-h2D_Sen1-AID
treatment: Auxin
chip antibody: RAD52 (D. Bishop Lab)
|
| Treatment protocol |
Cells were treated with 0.5uM Auxin where indicated for 4h, or with 2% galactose where indicated.
|
| Growth protocol |
Cells were grown in YEPD till OD600=0.5.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were fixed with paraformaldehyde (final 1%) for 1h. Glycine was added to stop the reaction at 0.125M for 10’. After cell lysis, chromatin was sheared 20 times for 45 s each using a Covaris S2.
The library was prepared using the Accel-NGS 1S Plus DNA Library Kit (Swift Bioscience) following the manufacturer protocol.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
ChIP DNA
|
| Data processing |
The sequencing files were aligned to the SacCer3 yeast genome using Bowtie2 tool using standard parameters.
Peak regions were called using MACS2 tool using the standard parameters.
Genome_build: SacCer3
Supplementary_files_format_and_content: *.bed: Bed files include the peak regions using MACS2.
|
| |
|
| Submission date |
Feb 13, 2018 |
| Last update date |
Jul 18, 2018 |
| Contact name |
lorenzo costantino |
| Organization name |
university of california, berkeley
|
| Department |
MCB
|
| Lab |
KOSHLAND
|
| Street address |
16 Barker Hall # 3202
|
| City |
Berkeley |
| State/province |
CA |
| ZIP/Postal code |
94720-3202 |
| Country |
USA |
| |
|
| Platform ID |
GPL21656 |
| Series (1) |
| GSE110575 |
Genome-wide Map of R-Loop-Induced Damage Reveals How a Subset of R-Loops Contributes to Genomic Instability |
|
| Relations |
| BioSample |
SAMN08533499 |
| SRA |
SRX3697531 |
