|
| Status |
Public on Oct 21, 2014 |
| Title |
Scc2-4 +break IP |
| Sample type |
SRA |
| |
|
| Source name |
Scc2-4 +break IP
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
strain: LS148
genotype/variation: Scc2-4
condition: break Chr. VI
chip antibody: anti-flag antibody
chip antibody: Sigma
chip antibody: F3165
|
| Treatment protocol |
Log phase yeast cells were arrested in G2/M. The temperature was raised and 30 minutes later galactose was added to induce one DSB in cells containing the recognition site for the HO enzyme. Ninety minutes later, cells were harvested.
|
| Growth protocol |
YEP media supplemented with 2% raffinose
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from sonicated nuclei and Scc1 flag tagged DNA complexes were isolated with anti-flag antibody (Sigma F3165)
The 5500 SOLiD™ Fragment Library Core Kit
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
AB SOLiD System |
| |
|
| Description |
Library8
|
| Data processing |
SOLiD raw data were converted to csfasta and qaul files and mapped with bowtie.
Basecalls performed using Corona
mapped to S. cerevisiae whole genome using bowtie v0.12.2 with parameters -n3 -m10
The result files were formatted sam type with the option --sam.
Then, sam files were converted to wig files with the script “bed2wig.py”(https://github.com/daler/rdbio-scripts/blob/master/sequenceFiles/bed2wig.py)
Data were visualized using Cairo
Genome_build: sacCer1
Supplementary_files_format_and_content: wig files
|
| |
|
| Submission date |
Oct 20, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Lena Ström |
| E-mail(s) |
lena.strom@ki.se
|
| Phone |
+46852487043
|
| Organization name |
Karolinska Institutet
|
| Department |
Cell and Molecular Biology
|
| Lab |
Lena Ström lab
|
| Street address |
Berzelius väg 35
|
| City |
Stockholm |
| ZIP/Postal code |
17177 |
| Country |
Sweden |
| |
|
| Platform ID |
GPL10577 |
| Series (2) |
| GSE62493 |
Inactivation of the Budding Yeast Cohesin Loader Scc2 alters Gene Expression both Globally and in Response to a Single DNA Double Strand Break [ChIP-seq] |
| GSE62494 |
Inactivation of the Budding Yeast Cohesin Loader Scc2 alters Gene Expression both Globally and in Response to a Single DNA Double Strand Break |
|
| Relations |
| BioSample |
SAMN03120680 |
| SRA |
SRX736197 |
