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| Status |
Public on Jun 20, 2018 |
| Title |
Stereotyped p53 binding tuned by chromatin accessibility |
| Organism |
Homo sapiens |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
Expression profiling by high throughput sequencing
Other
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| Summary |
We accessed the cell type specificity of p53 by directly measuring DNA binding in twelve cell lines in response to ionizing radiation. We find that that vast majority of binding sites are occupied across all cells lines uniformly, in contrast to p53 regulated gene expression which shows great diversity in the same context. We further identify a subset of p53 binding sites that are more restricted, appearing in one or a few cell lines. We find that chromatin accessibility explains much of these differential binding events.
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| Overall design |
p53 DNA binding was measured in twelve cell lines after IR by ChIPseq. The transcriptional response of each of the twelve lines was also measured by mRNAseq. To explore the influence of chromatin accessability p53 binding was compared to ATAC-seq data from two cell lines.
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| Contributor(s) |
Stewart-Ornstein J, Hafner A, Lahav G |
| Citation(s) |
32070277 |
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| Submission date |
Jun 21, 2017 |
| Last update date |
Mar 02, 2020 |
| Contact name |
Jacob Stewart-Ornstein |
| E-mail(s) |
jas632@pitt.edu, jacob@stewart-ornstein-lab.com
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| Organization name |
University of Pittsburgh, School of Medicine
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| Department |
computational and systems biology
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| Lab |
Stewart-Ornstein
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| Street address |
UPMC Hillman Cancer Center, 5117 Centre Avenue
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| City |
Pittsburgh |
| State/province |
PA |
| ZIP/Postal code |
15213 |
| Country |
USA |
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| Platforms (1) |
| GPL18573 |
Illumina NextSeq 500 (Homo sapiens) |
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| Samples (66)
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| GSM2677370 |
LOXIMVI ATACseq |
| GSM2677371 |
MCF7_Input |
| GSM2677372 |
MCF7 p53 ChIPseq, 2hrs 4GY |
| GSM2677373 |
LOXIMVI p53 ChIPseq, 2hrs 4GY |
| GSM2677374 |
UO31 p53 ChIPseq, 2hrs 4GY |
| GSM2677375 |
A498 p53 ChIPseq, 2hrs 4GY |
| GSM2677376 |
U2OS p53 ChIPseq, 2hrs 4GY |
| GSM2677377 |
SKMEL5 p53 ChIPseq, 2hrs 4GY |
| GSM2677378 |
MALME3 p53 ChIPseq, 2hrs 4GY |
| GSM2677379 |
H460 p53 ChIPseq, 2hrs 4GY |
| GSM2677380 |
A549 p53 ChIPseq, 2hrs 4GY |
| GSM2677381 |
HCT116 p53 ChIPseq, 2hrs 4GY |
| GSM2677382 |
UACC62 p53 ChIPseq, 2hrs 4GY |
| GSM2677383 |
UACC257 p53 ChIPseq, 2hrs 4GY |
| GSM2677384 |
MCF7_p53ChIPseq_nutlin_2hr |
| GSM2677385 |
UACC257_p53ChIPseq_nutlin_2hr |
| GSM2677386 |
RPE_p53ChIPseq_2h_4GY |
| GSM2677387 |
MCF7_RNA_NT |
| GSM2677388 |
LOXIMVI_RNA_NT |
| GSM2677389 |
UO31_RNA_NT |
| GSM2677390 |
A498_RNA_NT |
| GSM2677391 |
U2OS_RNA_NT |
| GSM2677392 |
SKMEL5_RNA_NT |
| GSM2677393 |
MALME3_RNA_NT |
| GSM2677394 |
H460_RNA_NT |
| GSM2677395 |
A549_RNA_NT |
| GSM2677396 |
HCT116_RNA_NT |
| GSM2677397 |
UACC257_RNA_NT |
| GSM2677398 |
UACC62_RNA_NT |
| GSM2677399 |
MCF7_mRNA, 3hrs 4Gy |
| GSM2677400 |
LOXIMVI_mRNA, 3hrs 4Gy |
| GSM2677401 |
UO31_mRNA, 3hrs 4Gy |
| GSM2677402 |
A498_mRNA, 3hrs 4Gy |
| GSM2677403 |
U2OS_mRNA, 3hrs 4Gy |
| GSM2677404 |
SKMEL5_mRNA, 3hrs 4Gy |
| GSM2677405 |
MALME3_mRNA, 3hrs 4Gy |
| GSM2677406 |
H460_mRNA, 3hrs 4Gy |
| GSM2677407 |
A549_mRNA, 3hrs 4Gy |
| GSM2677408 |
HCT116_mRNA, 3hrs 4Gy |
| GSM2677409 |
UACC257_mRNA, 3hrs 4Gy |
| GSM2677410 |
UACC62_mRNA, 3hrs 4Gy |
| GSM2740042 |
invitro_background |
| GSM2740043 |
invitro_p53IP |
| GSM2740044 |
MCF_Decitabine_ATACseq |
| GSM2740045 |
MCF_minus_Decitabine_p53chip |
| GSM2740046 |
MCF_plus_Decitabine_p53chip |
| GSM3771330 |
A549_NT_nutin_p53cs_r1 |
| GSM3771331 |
A549_NT_nutin_p53cs_r2 |
| GSM3771332 |
A549_TGFB_nutin_p53cs_r1 |
| GSM3771333 |
A549_TGFB_nutin_p53cs_r2 |
| GSM3771334 |
A549_input_nt |
| GSM3771335 |
A549_input_tgfb |
| GSM3771336 |
A549_NT_RNAseq_r1 |
| GSM3771337 |
A549_NT_RNAseq_r2 |
| GSM3771338 |
A549_NT_RNAseq_r3 |
| GSM3771339 |
A549_NUT_RNAseq_r1 |
| GSM3771340 |
A549_NUT_RNAseq_r2 |
| GSM3771341 |
A549_NUT_RNAseq_r3 |
| GSM3771342 |
A549_TGFB_RNAseq_r1 |
| GSM3771343 |
A549_TGFB_RNAseq_r2 |
| GSM3771344 |
A549_TGFB_RNAseq_r3 |
| GSM3771345 |
A549_TGFB_NUT_RNAseq_r1 |
| GSM3771346 |
A549_TGFB_NUT_RNAseq_r2 |
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| Relations |
| BioProject |
PRJNA391270 |
| SRA |
SRP110004 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE100292_GEO_2A.bed.gz |
130.4 Kb |
(ftp)(http) |
BED |
| GSE100292_GEO_2B.bed.gz |
133.2 Kb |
(ftp)(http) |
BED |
| GSE100292_chipseq.tsv.gz |
557.6 Kb |
(ftp)(http) |
TSV |
| GSE100292_chipseq_tgfb.bed.gz |
134.6 Kb |
(ftp)(http) |
BED |
| GSE100292_mRNAseq.tsv.gz |
907.2 Kb |
(ftp)(http) |
TSV |
| GSE100292_rnaseq_tgfb.tsv.gz |
583.5 Kb |
(ftp)(http) |
TSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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