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Sample GSM5089947 Query DataSets for GSM5089947
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.
 
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
 
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

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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