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| Status |
Public on Nov 06, 2018 |
| Title |
Genome-wide transcription factor binding and histone mark profiling in pluripotent and lineage-committed cells |
| Organism |
Homo sapiens |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
Purpose: Assess changes in p63 binding in human embryonic stem cells and surface ectoderm; evaluate differences in the following histone marks: H3K27me3, H3K27ac, H3K4me1, and H3K4me3 in the surface ectoderm with and without p63; and examine changes in H3K27me3 between human embyronic stem cells and surface ectoderm with and without p63.
Methods: p63 ChIP-seq libraries were generated in p63 gain-of-function human embryonic stem cells and wild-type surface ectoderm. H3K27me3 ChIP-seq libraries were generated in wild-type and p63 gain-of-function human embryonic stem cells as well as wild-type and p63 knockout surface ectoderm. H3K27ac, H3K4me1, and H3K4me3 ChIP-seq libraries were generated in wild-type and p63 knockout surface ectoderm. All ChIP-seq experiments were performed in duplicate and sequenced on Illumina NextSeq 500 sequencer. To ensure quality reads, fastq files were analyzed using FASTQC. Bowtie was used for read mapping and the parameters were as follows: -p 24 -S -a -m 1 --best --strata. For peak calling using MACS2, default settings were specified with a p-value of 0.05. To ensure quality peaks, IDR was run on all files, specifying FDR of 1% or 5% (or 10% for some broadPeak histone marks).
Results: Limited changes in p63 binding in human embryonic stem cells and surface ectoderm; global loss of H3K37me3 without p63 in the surface ectoderm; limited differences in H3K27ac, H3K4me1, and H3K4me3 +/- p63 in the surface ectoderm; and increase in H3K27me3 with ectopic expression of p63 in human embryonic stem cells.
Conclusion: p63 is able to bind it's surface ectoderm target sites regardless of the epigenetic landscape; p63 promotes H3K27me3 accumulation; and p63 does not regulate histone marks H3K27ac, H3K4me1, or H3K4me3
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| Overall design |
p63, H3K27me3, H3K27ac, H3K4me1, and H3K4me3 ChIP-seq profiles were generated in duplicate by deep sequencing on Illumina NextSeq 500 sequencer
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| Contributor(s) |
Melo SP, Pattison JM, Piekos SN, Oro AE |
| Citation(s) |
30397335 |
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| Submission date |
Nov 04, 2018 |
| Last update date |
Mar 26, 2019 |
| Contact name |
Anthony E Oro |
| Organization name |
Stanford University
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| Street address |
269 Campus Dr, CCSR 2140
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| City |
Stanford |
| State/province |
CA |
| ZIP/Postal code |
94305 |
| Country |
USA |
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| Platforms (1) |
| GPL18573 |
Illumina NextSeq 500 (Homo sapiens) |
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| Samples (27)
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| GSM3455873 |
p63 ChIP-seq WT Day 7 - Replicate 2 |
| GSM3455874 |
p63 ChIP-seq KC - Replicate 1 |
| GSM3455875 |
p63 ChIP-seq KC - Replicate 2 |
| GSM3455876 |
H3K27me3 ChIP-seq WT Day 0 - Replicate 1 |
| GSM3455877 |
H3K27me3 ChIP-seq WT Day 0 - Replicate 2 |
| GSM3455878 |
H3K27me3 ChIP-seq p63GOF Day 0 - Replicate 1 |
| GSM3455879 |
H3K27me3 ChIP-seq p63GOF Day 0 - Replicate 2 |
| GSM3455880 |
H3K27me3 ChIP-seq WT Day 7 - Replicate 1 |
| GSM3455881 |
H3K27me3 ChIP-seq WT Day 7 - Replicate 2 |
| GSM3455882 |
H3K27me3 ChIP-seq p63KO Day 7 - Replicate 1 |
| GSM3455883 |
H3K27me3 ChIP-seq p63KO Day 7 - Replicate 2 |
| GSM3455884 |
H3K27ac ChIP-seq WT Day 7 - Replicate 1 |
| GSM3455885 |
H3K27ac ChIP-seq WT Day 7 - Replicate 2 |
| GSM3455886 |
H3K27ac ChIP-seq p63KO Day 7 - Replicate 1 |
| GSM3455887 |
H3K27ac ChIP-seq p63KO Day 7 - Replicate 2 |
| GSM3455888 |
H3K4me1 ChIP-seq WT Day 7 - Replicate 1 |
| GSM3455889 |
H3K4me1 ChIP-seq WT Day 7 - Replicate 2 |
| GSM3455890 |
H3K4me1 ChIP-seq p63KO Day 7 - Replicate 1 |
| GSM3455891 |
H3K4me1 ChIP-seq p63KO Day 7 - Replicate 2 |
| GSM3455892 |
H3K4me3 ChIP-seq WT Day 7 - Replicate 1 |
| GSM3455893 |
H3K4me3 ChIP-seq WT Day 7 - Replicate 2 |
| GSM3455894 |
H3K4me3 ChIP-seq p63KO Day 7 - Replicate 1 |
| GSM3455895 |
H3K4me3 ChIP-seq p63KO Day 7 - Replicate 2 |
| GSM3455896 |
Input |
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| This SubSeries is part of SuperSeries: |
| GSE119997 |
RA and BMP4 cooperate with p63 to alter chromatin dynamics during surface epithelial commitment |
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| Relations |
| BioProject |
PRJNA503743 |
| SRA |
SRP167795 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE122128_RAW.tar |
4.7 Mb |
(http)(custom) |
TAR (of BED, BROADPEAK, NARROWPEAK) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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