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Series GSE243999 Query DataSets for GSE243999
Status Public on Jun 28, 2024
Title Mouse models to investigate in situ cell fate decisions induced by TP53 and other factors (CUT&RUN)
Organism Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary We developed triple-FLAG TRP53 knock-in mice for TRP53 pull-down and two TRP53 response reporter mice, knocking tdTomato or GFP into the Puma/Bbc3 or p21 gene loci, respectively. By crossing the reporter mice onto a TRP53-deficient background, we could show that these reporters reliably inform on TRP53-dependent and TRP53-independent initiation of the apoptotic as well as the cell cycle arrest/senescence programs in vitro and even in vivo.
 
Overall design FLAG-TRP53 pulldown was used for CUT&RUN analysis to identify binding of TRP53 to its target genes. Murine dermal fibroblasts (MDFs) were generated from tails of 8-12 weeks-old mice from FLAG-Trp53 KI/KI, FLAG-Trp53 KI/+, and WT (negative control) genotypes and were treated for 6h in vitro with either Nutlin-3a or DMSO (vehicle control). Cell extracts were made and subjected to pulldown using an antibody against P53-FLAG antibody.
 
Contributor(s) Smyth GK, Baldoni PL
Citation(s) 39160273
Submission date Sep 25, 2023
Last update date Sep 27, 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
 
Platforms (1)
GPL30172 NextSeq 2000 (Mus musculus)
Samples (23)
GSM7804557 MDF from KI-KI mice treated with DMSO - Replicate 1
GSM7804558 MDF from KI-KI mice treated with DMSO - Replicate 2
GSM7804559 MDF from KI-KI mice treated with DMSO - Replicate 3
Relations
BioProject PRJNA1020858

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE243999_KI-KI_DMSO.bigWig 275.5 Mb (ftp)(http) BIGWIG
GSE243999_KI-KI_DMSO_peaks.narrowPeak.gz 255.0 Kb (ftp)(http) NARROWPEAK
GSE243999_KI-KI_Nutlin.bigWig 182.0 Mb (ftp)(http) BIGWIG
GSE243999_KI-KI_Nutlin_peaks.narrowPeak.gz 277.5 Kb (ftp)(http) NARROWPEAK
GSE243999_KI-WT_DMSO.bigWig 122.8 Mb (ftp)(http) BIGWIG
GSE243999_KI-WT_DMSO_peaks.narrowPeak.gz 51.1 Kb (ftp)(http) NARROWPEAK
GSE243999_KI-WT_Nutlin.bigWig 165.8 Mb (ftp)(http) BIGWIG
GSE243999_KI-WT_Nutlin_peaks.narrowPeak.gz 109.4 Kb (ftp)(http) NARROWPEAK
GSE243999_WT-WT_DMSO.bigWig 121.3 Mb (ftp)(http) BIGWIG
GSE243999_WT-WT_DMSO_peaks.narrowPeak.gz 7.7 Kb (ftp)(http) NARROWPEAK
GSE243999_WT-WT_Nutlin.bigWig 132.8 Mb (ftp)(http) BIGWIG
GSE243999_WT-WT_Nutlin_peaks.narrowPeak.gz 7.5 Kb (ftp)(http) NARROWPEAK
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