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Sample GSM7804557 Query DataSets for GSM7804557
Status Public on Jun 28, 2024
Title MDF from KI-KI mice treated with DMSO - Replicate 1
Sample type SRA
 
Source name Mouse tail skin
Organism Mus musculus
Characteristics tissue: Mouse tail skin
cell type: MDF
antibody: Anti-FLAG M2 (Sigma-Aldrich, F1804)
strain: p53-FLAG
developmental stage: adult (8-12 weeks of age)
mouse pool: B
Sex: male
sequencing run: 26-Aug-2022; Read Length: 161 bp; Cycle Kit: P1 300
Extracted molecule genomic DNA
Extraction protocol 500,000 MDFs were plated and left to settle for 24 h in an incubator with 10% CO2 at 37°C. Medium was replaced with medium containing nutlin-3a (10 μM, Cayman Chemicals #18585) or DMSO (vehicle control) and cells incubated for 6 h. Adherent cells were dissociated with trypsin (0.25 mg/mL, Sigma #T4174), keeping both the supernatant and the trypsinised fractions for analysis. CUT&RUN was performed using the CUTANA ChIC/CUT&RUN kit v2 (Epicypher, 14-1408) as per the manufacture’s protocol. Nuceli were isolated prior to the start of the assay. Nuclei were bound to activated conA beads. Samples were incubated with 0.5 μg of anti-FLAG antibody (Sigma, F1804) overnight. DNA was cut using pAG-MNase, and unbound fragments washed away. Bound chromatin was release from the beads, and DNA was purified.
Total recovered DNA was taken into library preparation using the NEBNext Ultra II DNA library Prep Kit for Illumina (#E7645L).
CUT&RUN
 
Library strategy OTHER
Library source genomic
Library selection other
Instrument model NextSeq 2000
 
Data processing Libraries were sequenced on an Illumina NextSeq 2000 to produce paired-end reads.
Reads were aligned to the mouse genome mm39 with R/Bioconductor Rsubread package and its align function.
Bam files from biological replicates were merged with samtools prior to creating BigWig files for each drug-genotype combination.
Assembly: mm39
Supplementary files format and content: BigWig files were created with the deepTools BamCoverage program with reads per genomic content (RPGC) normalization in 10 bp windows. Duplicated reads, reads from sex and mitochondrial chromosomes, and reads overlapping ENCODE blacklisted regions from the mm39 genome were discarded for normalization purposes
Supplementary files format and content: narrowPeak files (in BED format) are peak regions called by MACS2 for each genotype-drug combination. Biological replicates were combined by the MACS2 program during the peak calling step.
 
Submission date Sep 25, 2023
Last update date Jun 28, 2024
Contact name Gordon K Smyth
E-mail(s) smyth@wehi.edu.au
Phone (+61 3) 9345 2326
Fax (+61 3) 9347 0852
URL http://www.wehi.edu.au
Organization name Walter and Eliza Hall Institute of Medical Research
Department Bioinformatics
Lab Smyth
Street address 1G Royal Pde
City Parkville
State/province Vic
ZIP/Postal code 3052
Country Australia
 
Platform ID GPL30172
Series (1)
GSE243999 Mouse models to investigate in situ cell fate decisions induced by TP53 and other factors (CUT&RUN)
Relations
BioSample SAMN37536225
SRA SRX21882213

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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