|
| Status |
Public on Jan 12, 2019 |
| Title |
WT 0h RPA |
| Sample type |
SRA |
| |
|
| Source name |
WT 0h RPA
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
background strain: W303
genotype/variation: WT
time point: before DSB induction
antibody: RPA
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
bead beater lysis, shearing by sonication, RNAseA digest, de-crosslinking, phenol-chloroform extraction
MicroPlex Library Preparation kit v2 (Diagenode)
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 1500 |
| |
|
| Description |
input used: input_WT_0
IP against RPA
|
| Data processing |
Raw datas quality was check using the fastqc tool (v. 0.11.2)
the raw data was mapped to the S. cerevisiae genome, excluding multimapped reads (option -m 1)
Using the R (v. 3.22) package GenomicRanges (v. 1.22) the files converted into binned table with a windows size of 1000bp.
the regions in the bam files overlapped the binned regions of the genome were normalized using the TMM normalisation from the edgeR packge (v. 3.12.0)
the table were than converted into wig files for better visulization
Genome_build: Ensembl, build R64-1-1
Supplementary_files_format_and_content: wig files were generated using the R software suite.
|
| |
|
| Submission date |
Jan 11, 2019 |
| Last update date |
Jan 13, 2019 |
| Contact name |
Susanne Charlotte Sophie Bantele |
| E-mail(s) |
sbantele@biochem.mpg.de
|
| Organization name |
Max Planck Institute of Biochemistry
|
| Department |
NWG
|
| Lab |
DNA REP (Pfander)
|
| Street address |
Am Klopferspitz 18
|
| City |
Martinsried/Munich |
| State/province |
Bavaria |
| ZIP/Postal code |
82152 |
| Country |
Germany |
| |
|
| Platform ID |
GPL18085 |
| Series (1) |
| GSE124948 |
Quantitative sensing and signalling of single-stranded DNA during the DNA damage response |
|
| Relations |
| BioSample |
SAMN10724604 |
| SRA |
SRX5241171 |
