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GSE46240

GSE GEO Potentially related
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Global genomic profiling of p53-regulated genes

Organism: Mus musculus
Platform: GPL9185
Samples: 14
Experiment Types:
Genome binding/occupancy profiling by high throughput sequencing Expression profiling by high throughput sequencing
Submitted: Apr 20 2013
Last Updated: Jul 31 2019
Status: Public on Apr 21 2013
Contact: Stephano,,Spano Mello (Stanford University)

Relations

BioProject: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA198448 SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRP021219

Summary

p53 is a critical tumor suppressor and works as a stress-induced transcription factor to induce target genes mediating apoptosis, cell cycle arrest and senescence or other responses. To gain new insights into p53 biology, we used high-throughput sequencing to analyze global p53 transcriptional networks in primary mouse embryo fibroblasts in response to DNA damage. ChIP-sequencing reveals 4785 p53-bound sites in the genome located near 3193 genes involved in diverse biological processes. RNA-sequencing analysis shows that only a subset of p53-bound genes is transcriptionally regulated, yielding a list of 432 p53-bound and regulated genes. Furthermore, we define a list of 1269 basal-p53 regulated genes, of which 253 are p53-bound and basal-p53 regulated.

Overall Design

ChIP-seq was performed to determine the genome-wide p53 binding sites in doxorubicin-treated primary MEFs. RNA-seq was used to define differentially expressed genes in response to DNA damage in wild-type and p53-/- MEFs, and basal p53 regulated genes by deriving differentially expressed genes between untreated wild-type and p53-/- MEFs.

Analysis (5 steps)

View Data Processing
Processing steps for GSE46240
  1. ChIP-seq and RNA-seq reads were aligned to the mm9 genome assembly using DNAnexus.
  2. For ChIP-seq: Peaks were called using the DNAnexus ChIP-seq analyses tool with the following specifications: peak enrichment >20, peak-to background enrichment >3, a minimum ratio between uniquely and repetitively mapped reads of 3:1, a kernel bandwith of 30.0, FDR calculation enabled.
  3. Background was combined input reads and reads from p53 ChIP in p53-/- MEFs.
  4. For RNA-seq: Tag counts were derived using the DNAnexus 3SEQ transcriptome-based quantification tool with the following specifications: Sense only, RefSeq genes.
  5. The DESeq library was used to normalize tag counts between samples and to call differentially expressed genes.

Supplementary Files (2)

GSE46240_ChIP-seq_peaks_p53_binding_sites.txt.gz Download
GSE46240_RAW.tar Download
GEO Samples (14)
GSM1126945 GSM1126946 GSM1126947 GSM1126948 GSM1126949 GSM1126950 GSM1126951 GSM1126952 GSM1126953 GSM1126954 GSM1126955 GSM1126956 GSM1126957 GSM1126958

Dataset Citations (2)

PubMed citation (PMID 23651856)
PubMed citation (PMID 25704813)

SRA Experiments (14) and Runs (14)

Total: 6338 MB
SRX270554 SRP021219 ChIP-Seq SINGLE
GSM1126945: p53 ChIP-seq_Sample 1; Mus musculus; ChIP-Seq
Sample: SRS415095
BioProject: PRJNA198448
BioSample: SAMN02054307
Platform: ILLUMINA
Instrument: Illumina Genome Analyzer
Organism: Mus musculus
Sample attributes
source_name: mouse embryo fibroblasts_p53 ChIP-seq_wt dox
strain: 129/Sv
cell type: mouse embryo fibroblast (MEF)
genotype/variation: wild-type
chip antibody: CM-5 (Vector labs, VP-P956)
treatment: 0.2ug/ml doxorubicin for 6h
Original files (1)
mouse embryo fibroblasts_p53 ChIP-seq_wt dox
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR832846 16685745 600686820 299.46 p53_ChIP-seq_wt_MEF.fastq.gz, SRR832846 SRA
SRX270555 SRP021219 ChIP-Seq SINGLE
GSM1126946: background_Sample 2; Mus musculus; ChIP-Seq
Sample: SRS415096
BioProject: PRJNA198448
BioSample: SAMN02054308
Platform: ILLUMINA
Instrument: Illumina Genome Analyzer
Organism: Mus musculus
Sample attributes
source_name: mouse embryo fibroblasts_background_wt dox
strain: 129/Sv
cell type: mouse embryo fibroblast (MEF)
genotype/variation: wild-type
chip antibody: none
treatment: 0.2ug/ml doxorubicin for 6h
Original files (1)
mouse embryo fibroblasts_background_wt dox
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR832847 16016755 576603180 281.6 input_wt_MEF.fastq.gz, SRR832847 SRA
SRX270556 SRP021219 ChIP-Seq SINGLE
GSM1126947: p53 ChIP-seq_Sample 3; Mus musculus; ChIP-Seq
Sample: SRS415097
BioProject: PRJNA198448
BioSample: SAMN02054309
Platform: ILLUMINA
Instrument: Illumina Genome Analyzer
Organism: Mus musculus
Sample attributes
source_name: mouse embryo fibroblasts_p53 ChIP-seq_p53-/- dox
strain: 129/Sv
cell type: mouse embryo fibroblast (MEF)
genotype/variation: p53-/-
chip antibody: CM-5 (Vector labs, VP-P956)
treatment: 0.2ug/ml doxorubicin for 6h
Original files (1)
mouse embryo fibroblasts_p53 ChIP-seq_p53-/- dox
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR832848 20616007 742176252 406.81 p53_ChIP-seq_p53KO_MEF.fastq.gz, SRR832848 SRA
SRX270557 SRP021219 ChIP-Seq SINGLE
GSM1126948: background_Sample 4; Mus musculus; ChIP-Seq
Sample: SRS415098
BioProject: PRJNA198448
BioSample: SAMN02054310
Platform: ILLUMINA
Instrument: Illumina Genome Analyzer
Organism: Mus musculus
Sample attributes
source_name: mouse embryo fibroblasts_background_p53-/- dox
strain: 129/Sv
cell type: mouse embryo fibroblast (MEF)
genotype/variation: p53-/-
chip antibody: none
treatment: 0.2ug/ml doxorubicin for 6h
Original files (1)
mouse embryo fibroblasts_background_p53-/- dox
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR832849 24491066 881678376 491.5 SRR832849, input_p53KO_MEF.fastq.gz SRA
SRX270558 SRP021219 RNA-Seq SINGLE
GSM1126949: wt ut rep1_Sample 5; Mus musculus; RNA-Seq
Sample: SRS415100
BioProject: PRJNA198448
BioSample: SAMN02054311
Platform: ILLUMINA
Instrument: Illumina Genome Analyzer
Organism: Mus musculus
Sample attributes
source_name: mouse embryo fibroblasts_wt ut
strain: 129/Sv
cell type: mouse embryo fibroblast (MEF)
genotype/variation: wild-type
treatment: untreated
Original files (1)
mouse embryo fibroblasts_wt ut
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR832850 16017990 576647640 306.06 wt_MEF_ ut_replicate-1.fastq.gz, SRR832850 SRA
SRX270559 SRP021219 RNA-Seq SINGLE
GSM1126950: wt dox rep1_Sample 6; Mus musculus; RNA-Seq
Sample: SRS415099
BioProject: PRJNA198448
BioSample: SAMN02054312
Platform: ILLUMINA
Instrument: Illumina Genome Analyzer
Organism: Mus musculus
Sample attributes
source_name: mouse embryo fibroblasts_wt dox
strain: 129/Sv
cell type: mouse embryo fibroblast (MEF)
genotype/variation: wild-type
treatment: 0.2ug/ml doxorubicin for 6h
Original files (1)
mouse embryo fibroblasts_wt dox
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR832851 19470988 700955568 394.67 wt_MEF_ dox_replicate-1.fastq.gz, SRR832851 SRA
SRX270560 SRP021219 RNA-Seq SINGLE
GSM1126951: wt ut rep2_Sample 7; Mus musculus; RNA-Seq
Sample: SRS415101
BioProject: PRJNA198448
BioSample: SAMN02054313
Platform: ILLUMINA
Instrument: Illumina Genome Analyzer
Organism: Mus musculus
Sample attributes
source_name: mouse embryo fibroblasts_wt ut
strain: 129/Sv
cell type: mouse embryo fibroblast (MEF)
genotype/variation: wild-type
treatment: untreated
Original files (1)
mouse embryo fibroblasts_wt ut
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR832852 18590743 669266748 370.77 wt_MEF_ ut_replicate-2.fastq.gz, SRR832852 SRA
SRX270561 SRP021219 RNA-Seq SINGLE
GSM1126952: wt dox rep2_Sample 8; Mus musculus; RNA-Seq
Sample: SRS415102
BioProject: PRJNA198448
BioSample: SAMN02054314
Platform: ILLUMINA
Instrument: Illumina Genome Analyzer
Organism: Mus musculus
Sample attributes
source_name: mouse embryo fibroblasts_wt dox
strain: 129/Sv
cell type: mouse embryo fibroblast (MEF)
genotype/variation: wild-type
treatment: 0.2ug/ml doxorubicin for 6h
Original files (1)
mouse embryo fibroblasts_wt dox
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR832853 19672370 708205320 397.55 wt_MEF_ dox_replicate-2.fastq.gz, SRR832853 SRA
SRX270562 SRP021219 RNA-Seq SINGLE
GSM1126953: wt ut rep3_Sample 9; Mus musculus; RNA-Seq
Sample: SRS415103
BioProject: PRJNA198448
BioSample: SAMN02054315
Platform: ILLUMINA
Instrument: Illumina Genome Analyzer
Organism: Mus musculus
Sample attributes
source_name: mouse embryo fibroblasts_wt ut
strain: 129/Sv
cell type: mouse embryo fibroblast (MEF)
genotype/variation: wild-type
treatment: untreated
Original files (1)
mouse embryo fibroblasts_wt ut
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR832854 15956162 574421832 298.83 wt_MEF_ ut_replicate-3.fastq.gz, SRR832854 SRA
SRX270563 SRP021219 RNA-Seq SINGLE
GSM1126954: wt dox rep3_Sample 10; Mus musculus; RNA-Seq
Sample: SRS415104
BioProject: PRJNA198448
BioSample: SAMN02054316
Platform: ILLUMINA
Instrument: Illumina Genome Analyzer
Organism: Mus musculus
Sample attributes
source_name: mouse embryo fibroblasts_wt dox
strain: 129/Sv
cell type: mouse embryo fibroblast (MEF)
genotype/variation: wild-type
treatment: 0.2ug/ml doxorubicin for 6h
Original files (1)
mouse embryo fibroblasts_wt dox
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR832855 17498991 629963676 335.23 wt_MEF_ dox_replicate-3.fastq.gz, SRR832855 SRA
SRX270564 SRP021219 RNA-Seq SINGLE
GSM1126955: p53-/- ut rep1_Sample 11; Mus musculus; RNA-Seq
Sample: SRS415106
BioProject: PRJNA198448
BioSample: SAMN02054317
Platform: ILLUMINA
Instrument: Illumina Genome Analyzer
Organism: Mus musculus
Sample attributes
source_name: mouse embryo fibroblasts_p53-/- ut
strain: 129/Sv
cell type: mouse embryo fibroblast (MEF)
genotype/variation: p53-/-
treatment: untreated
Original files (1)
mouse embryo fibroblasts_p53-/- ut
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR832856 29750198 1071007128 610.56 p53KO_MEF_ ut_replicate-1.fastq.gz, SRR832856 SRA
SRX270565 SRP021219 RNA-Seq SINGLE
GSM1126956: p53-/- dox rep1_Sample 12; Mus musculus; RNA-Seq
Sample: SRS415105
BioProject: PRJNA198448
BioSample: SAMN02054318
Platform: ILLUMINA
Instrument: Illumina Genome Analyzer
Organism: Mus musculus
Sample attributes
source_name: mouse embryo fibroblasts_p53-/- dox
strain: 129/Sv
cell type: mouse embryo fibroblast (MEF)
genotype/variation: p53-/-
treatment: 0.2ug/ml doxorubicin for 6h
Original files (1)
mouse embryo fibroblasts_p53-/- dox
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR832857 37620618 1354342248 766.12 p53KO_MEF_ dox_replicate-1.fastq.gz, SRR832857 SRA
SRX270566 SRP021219 RNA-Seq SINGLE
GSM1126957: p53-/- ut rep2_Sample 13; Mus musculus; RNA-Seq
Sample: SRS415108
BioProject: PRJNA198448
BioSample: SAMN02054319
Platform: ILLUMINA
Instrument: Illumina Genome Analyzer
Organism: Mus musculus
Sample attributes
source_name: mouse embryo fibroblasts_p53-/- ut
strain: 129/Sv
cell type: mouse embryo fibroblast (MEF)
genotype/variation: p53-/-
treatment: untreated
Original files (1)
mouse embryo fibroblasts_p53-/- ut
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR832858 30251251 1089045036 552.67 p53KO_MEF_ ut_replicate-2.fastq.gz, SRR832858 SRA
SRX270567 SRP021219 RNA-Seq SINGLE
GSM1126958: p53-/- dox rep2_Sample 14; Mus musculus; RNA-Seq
Sample: SRS415107
BioProject: PRJNA198448
BioSample: SAMN02054320
Platform: ILLUMINA
Instrument: Illumina Genome Analyzer
Organism: Mus musculus
Sample attributes
source_name: mouse embryo fibroblasts_p53-/- dox
strain: 129/Sv
cell type: mouse embryo fibroblast (MEF)
genotype/variation: p53-/-
treatment: 0.2ug/ml doxorubicin for 6h
Original files (1)
mouse embryo fibroblasts_p53-/- dox
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR832859 36595719 1317445884 825.77 p53KO_MEF_ dox_replicate-2.fastq.gz, SRR832859 SRA

Potentially Related Publications (1)

This accession was text-mined from the PMC full text of these publications. It may be referenced for comparison or reused from another study rather than generated for them.

Zmat3 Is a Key Splicing Regulator in the p53 Tumor Suppression Program.
Molecular cell · 2020

Data Files (14)

Accession File Name Stored Type Output Type Mapping Assembly Size Download
— input_wt_MEF.fastq.gz ChIP-Seq 281.6 MB link
— p53_ChIP-seq_p53KO_MEF.fastq.gz ChIP-Seq 406.8 MB link
— p53_ChIP-seq_wt_MEF.fastq.gz ChIP-Seq 299.5 MB link
— SRR832849 ChIP-Seq 491.5 MB link
— p53KO_MEF_ dox_replicate-1.fastq.gz RNA-Seq 766.1 MB link
— p53KO_MEF_ dox_replicate-2.fastq.gz RNA-Seq 825.8 MB link
— p53KO_MEF_ ut_replicate-1.fastq.gz RNA-Seq 610.6 MB link
— p53KO_MEF_ ut_replicate-2.fastq.gz RNA-Seq 552.7 MB link
— wt_MEF_ dox_replicate-1.fastq.gz RNA-Seq 394.7 MB link
— wt_MEF_ dox_replicate-2.fastq.gz RNA-Seq 397.5 MB link
— wt_MEF_ dox_replicate-3.fastq.gz RNA-Seq 335.2 MB link
— wt_MEF_ ut_replicate-1.fastq.gz RNA-Seq 306.1 MB link
— wt_MEF_ ut_replicate-2.fastq.gz RNA-Seq 370.8 MB link
— wt_MEF_ ut_replicate-3.fastq.gz RNA-Seq 298.8 MB link