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Sample GSM8721217 Query DataSets for GSM8721217
Status Public on Jan 10, 2025
Title 581_dTAG_H4K20me2_T0_rep3
Sample type SRA
 
Source name E14JU
Organism Mus musculus
Characteristics cell line: E14JU
cell type: embryonic stem cells
genotype: POLE4-dTAG, MCM2-2A clone 2
chip antibody: H4K20me2
Treatment protocol Cells were incubated in EdU media (f.c. 10 µm) for 10 min and then collected (T0). If treated with DMSO or dTAG, cells were incubated for 1uM dTAG or DMSO prior to incubation with EdU for 10 min and then either collected (T0).
Growth protocol ESCs were grown on gelatin-coated dishes in serum+LIF conditions at 37 °C with 5 % CO2. DMEM was supplied with fetal bovine serum (15 %), home-made LIF, non-essential amino acids, penicillin/streptomycin and beta-mercaptoethanol. Cells were passaged using Trypsin-EDTA or TrypLE. Drosophila S2-DRSC cells were cultivated in suspension in spinners using M3+BPYE media, 10% heat-inactivated FBS , and 1X penicillin/streptomycin . Cells were incubated at 25°C with 5% CO2.
Extracted molecule genomic DNA
Extraction protocol After the appropriate treatment, 1% formaldehyde for 10 min. Then, glycine was added to quench the reaction and cells were subsequently lysed. Sonication was performed on isolated nuclei using a Covaris E220. DNA fragments were immunoprecipitated, purified fragments were biotinylated, libraries were prepared, EdU-biotin fragments were pulled-down and sequenced.
Libraries were costructed using the KAPA Hyperprep kit and Illumina-compatible indexed adapters (Pentabase) following manufacturer’s instruction. For the amplification step, 11 PCR cycles were used. Subsequently, the DNA underwent size selection using Agencourt AMPure XP beads (Beckman Coulter, A63881) to obtain fragments between 200-700 bp. Libraries were validated using Agilent Fragment Analyzer.
 
Library strategy OTHER
Library source genomic
Library selection other
Instrument model NextSeq 2000
 
Description Library name: Sample76
581_dTAG_H4K20me2_RRPM_merged.bw
Data processing adapters and low quality reads were filtered with TrimGalore (v0.0.6)
reads were mapped to the genome with bowtie2 (v2.4.2) and uniquely mapped peaks kept using samtools (v1.12)
duplicate reads were removed with picard (version 2.26.10)
bam files were processed to bigwig for RPM by bamCoverage or RRPM in SeqMonk
bigwigs: bam files were normalized to the number of million of reads (RPM) in 50 bp bins with bamCoverage
Assembly: mm10 and dm6
Supplementary files format and content: bigwigs
Library strategy: CHOR-seq
 
Submission date Jan 09, 2025
Last update date Jan 10, 2025
Contact name Anja Groth
E-mail(s) anja.groth@cpr.ku.dk
Organization name Novo Nordisk Foundation Center for Protein Research
Street address Blegdamsvej 3B
City Copenhagen
ZIP/Postal code 2200
Country Denmark
 
Platform ID GPL30172
Series (2)
GSE270291 Disabling leading and lagging strand histone transmission results in parental histones loss and reduced cell plasticity and viability [ChOR-seq]
GSE270297 Disabling leading and lagging strand histone transmission results in parental histones loss and reduced cell plasticity and viability
Relations
BioSample SAMN46179565
SRA SRX27297577

Supplementary file Size Download File type/resource
GSM8721217_581_dTAG_H4K20me2_T0_r3_t2_R1.srt.pairs.uminodup.uniq.sorted.mm10.bw 159.2 Mb (ftp)(http) BW
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