|
Status |
Public on Nov 08, 2023 |
Title |
IP_KO_Tal_II |
Sample type |
SRA |
|
|
Source name |
IP_KO_Tal
|
Organism |
Mus musculus |
Characteristics |
strain: C57BL/6JRj cell type: mouse embryonic stem cells genotype: KO; Tdg-depleted treatment: 5 nM Talazoparib for 24 h
|
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.
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Library strategy |
OTHER |
Library source |
genomic |
Library selection |
other |
Instrument model |
Illumina NextSeq 500 |
|
|
Description |
BSSE_QGF_132506_H3MGGBGXF_1_IP_KO_Tal_2_ATGTCA_S7_R*_001_MM BSSE_QGF_132506_H2JC5BGXF_1_IP_KO_Tal_2_ATGTCA_S7_R*_001_MM processed data file: SSB_KO_Tal.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
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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 |
SAMN17957114 |
SRA |
SRX10120527 |