|
| Status |
Public on Oct 28, 2016 |
| Title |
RNA-DNA hybrid ChIP-exo, Induced, Rep1 |
| Sample type |
SRA |
| |
|
| Source name |
Yeast DNA
|
| Organism |
Schizosaccharomyces pombe |
| Characteristics |
strain: DSB-PpoI system, Rnh1del-Rnh201del
ppoi induction: ON
antibody: S9.6
protein tag: none
beads: Protein A-G mix
|
| Treatment protocol |
For treatment protocol please refer to the Materials and Methods.
|
| Growth protocol |
Cultures were grown in full media (YEA) at 30ºC to O.D. of 0.8.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
For extraction and library preparation protocol please refer to the Materials and Methods. (ChIP-exo)
For extraction and library preparation protocol please refer to the Materials and Methods. (ChIP-exo)
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Demultiplexing and removal of adapter conatmination was done in one step.
Reads were mapped to modified S. pombe genome, with Bowtie2 software. (v2.2.5)
PCR duplicates were filtered out and genome-wide coverage was calculated using R Bioconductor packages.
Datasets were normalised for coverage over Chr I.
Genome_build: ASM294v2.29 with insertion at position 1231078. Insert length is 1842 bases. Insert sequence (txt file), modified genome (fasta format) and modified annotations (bedfile) are included in the upload.
Supplementary_files_format_and_content: BigWig format containing normalised genome-wide coverage for forward (.fw) and for reverse (.rev) strands separately
|
| |
|
| Submission date |
Apr 18, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Tamas Fischer |
| E-mail(s) |
tamas.fischer@bzh.uni-heidelberg.de
|
| Phone |
+49 6221 544728
|
| Organization name |
Biochemie Zentrum Heidelebrg
|
| Department |
BZH
|
| Lab |
AG Fischer
|
| Street address |
Im Neuenheimer Feld 328
|
| City |
Heidelberg |
| ZIP/Postal code |
69120 |
| Country |
Germany |
| |
|
| Platform ID |
GPL13988 |
| Series (2) |
| GSE80398 |
Transient RNA-DNA Hybrids Are Required for Efficient Double-Strand Break Repair |
| GSE84883 |
Transient RNA-DNA Hybrids Are Required for Efficient Double-Strand Break Repair |
|
| Relations |
| BioSample |
SAMN04867740 |
| SRA |
SRX1711754 |
