|
| Status |
Public on Jun 25, 2021 |
| Title |
ML3289 (OAY470 LEU2::-gal1/10-GapR-3xFLAG) in raffinose and induced with galactose, input |
| Sample type |
SRA |
| |
|
| Source name |
Saccharomyces cerevisiae
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
growth stage: exponential phase
strain: ML3289
media: YEP + 2% raffinose
|
| Treatment protocol |
If indicated cells were treated with alpha-factor. Cells were subsequently induced with 2% galactose for 6 hr.
|
| Growth protocol |
Strains were grown as described, and 2% galactose was added for 6 hr to induce GapR. Cells then fixed by the addition 1% formaldehyde (final concentrations).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP was performed as previously reported (Guo et al, 2018).
Libraries were constructed by end repairing DNA with T4 DNA polymerase (NEB), T4 PNK (NEB), and Klenow large fragment (NEB). 3’ overhangs were added with Klenow (3'→5' exo-) (NEB). Y-shaped Illumina adapters were ligated onto the DNA, and libraries were amplified with Kapa HiFi Polymerase (Kapa Biosystems). Libraries were size selected to be 200-500 bp.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Strains were grown in YEP+2% raffinose to OD 0.05, and 2% galactose was added. Cells were grown for 6 hr (OD ~1.0) and then fixed by the addition 1% formaldehyde (final concentrations). ChIP was then performed as described.
|
| Data processing |
Reads were aligned to Saccharomyces cerevisiae (S288C Scer3) with bowtie2 (version 2.1.0) using the default parameters.
Bowtie alignments were converted to wiggle files with custom Python scripts. The position of each alignment is evenly distributed over the length of the read.
Genome_build: Scer3
Supplementary_files_format_and_content: Tab delimited files, columns containing index positions, chromosome, chromosome positions, number of reads, and normalized number of reads.
|
| |
|
| Submission date |
Jan 04, 2021 |
| Last update date |
Aug 22, 2021 |
| Contact name |
Monica S Guo |
| E-mail(s) |
msguo@uw.edu
|
| Organization name |
University of Washington
|
| Department |
Microbiology
|
| Lab |
Guo
|
| Street address |
750 Republican St
|
| City |
Seattle |
| State/province |
WA |
| ZIP/Postal code |
98109 |
| Country |
USA |
| |
|
| Platform ID |
GPL19756 |
| Series (2) |
| GSE152881 |
High-resolution, genome-wide mapping of positive supercoiling in chromosomes [yChIP] |
| GSE152882 |
High-resolution, genome-wide mapping of positive supercoiling in chromosomes |
|
| Relations |
| BioSample |
SAMN17208734 |
| SRA |
SRX9773810 |
