|
| Status |
Public on Nov 08, 2023 |
| Title |
IP_WT_I |
| Sample type |
SRA |
| |
|
| Source name |
IP_WT
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6JRj
cell type: mouse embryonic stem cells
genotype: wild type
treatment: DMSO
|
| Treatment protocol |
ESCs were treated with 5 nM Talazoparib (Selleckchem, S7048) for 24 h prior to extraction.
|
| Growth protocol |
ESCs were cultured on gelatin-coated dishes under a controlled atmosphere (37°C, 5% CO2, 95% humidity) in serum-free 2i medium with 1000 U/ml LIF and without antibiotics. The 4-OHT to excise Tdg minigene (Sigma-Aldrich H7904) was dissolved in DMSO (stock 10 mM) and administered at 5 uM for 2 h before each experiment.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
~20 mio cells were harvested from a 15 cm dish and genomic DNA was extracted with the genomic tips kit 100 (Qiagen). 50 ug of DNA were subjected to SSB-seq protocol. Briefly: Nick-translation was performed with E-coli Pol I at 16°C for 1 min, including DIG-dUTPs and ddNTPs to prevent exceeding polymerization. The labelled DNA was precipitated, purified and subsequently sonicated and digested with restriction enzymes to get rid of high-molecular DNA. The fragmented DNA was purified again and subjected to immunoprecipitation using an anti-DIG antibody (Roche 11333089001) and Protein G Dynabeads (Life Technologies). Immunoprecipitated DNA was purified with the ChIP DNA clean & concentrator kit (Zymo).
10 ng of each immunoprecipitated DNA and Input DNA were subjected to library construction with a KAPA HyperPrep Kit (Roche) using 8 cycles of amplification.
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
BSSE_QGF_132492_HTVWKBGXC_1_IP_WT_I_CGATGT_S2_R*_001_MM
BSSE_QGF_132492_HWNKLBGXC_1_IP_WT_I_CGATGT_S2_R*_001_MM
processed data file: SSB_WT_DMSO.txt.gz
|
| Data processing |
library strategy: Single-Strand Break (SSB)-Seq
Reads where aligned to the mouse genome (mm10 UCSC version) with bowtie2 (version 2.3.4.2) and extra options "--maxins 2000 --no-mixed --no-discordant --local --mm". Duplicates where marked with picard tools (version 2.9.2)
BAM files where filtered by removing reads falling into ENCODE blacklist regions (version 2014 + manual removal of high coverage regions) using Rsamtools (R version 3.6, Bioconductor version 3.10)
Peaks were called across all replicates of a sample group using HOMER (version 4.11) and “findPeaks” with specifying commands “-style histone -o auto” with the corresponding input as a control.
Genome_build: mm10
Supplementary_files_format_and_content: HOMER output files of detected SSB peaks called over the three replicates; columns: chrom, start, end, name, score, strand, signal value, -log10(p-value), -log10(q-value), peak ID
|
| |
|
| Submission date |
Feb 17, 2021 |
| Last update date |
Nov 08, 2023 |
| Contact name |
DBM Bioinformatics Core Facility |
| Phone |
+41612073541
|
| Organization name |
University of Basel
|
| Department |
Departement of Biomedicine
|
| Street address |
Hebelstrasse 20
|
| City |
Basel |
| State/province |
BS |
| ZIP/Postal code |
4053 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL19057 |
| Series (2) |
| GSE166963 |
Covalent PARylation of DNA base excision repair proteins regulates DNA demethylation |
| GSE166964 |
PARP inhibition induces cytotoxicity in mESCs by activating endogenous retroviruses. |
|
| Relations |
| BioSample |
SAMN17957132 |
| SRA |
SRX10120514 |
