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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Feb 18, 2015 |
| Title |
Global Reorganization of Chromatin Architecture during Embronic Stem Cell Differentiation |
| Organism |
Homo sapiens |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
Other
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| Summary |
The 3D organization of the genome is important for regulation of diverse nuclear processes ranging from transcription to DNA replication. Knowledge of the higher order chromatin structure is critical for understanding mechanisms of gene regulation by long-range control elements such as enhancers and insulators. We describe high resolution, genome-wide dynamic chromatin interaction maps in human embryonic stem cells (hESC) as they differentiate into four distinct embryonic cell lineages. Extensive reorganization of higher-order chromatin structure occurs during hESC differentiation. In this process, topological domains remain largely intact but inter-domain association patterns change dramatically, coincident with widespread changes in chromatin state and gene expression. Moreover, using proximity ligation sequencing to generate chromosome span haplotypes, widespread allele biased gene activities are detected. The allelic gene expression patterns can be correlated to epigenetic state at distal enhancers, supporting the role of these elements in regulating gene expression over a distance.
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| Overall design |
Two biological replicates of Hi-C experiment and one replicate of CTCF ChIP-Seq experiment in embryonic stem cells and 4 other differentiated cell-types from H1 cell line. Re-analysis of data from GSE16256 in an allele specific manner is linked as supplementary data.
Hi-C data generated in this study can be visualized at www.3dgenome.org.
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| Contributor(s) |
Dixon JR, Jung I, Selvaraj S, Ren B |
| Citation(s) |
25693564 |
| Submission date |
Nov 18, 2013 |
| Last update date |
Feb 22, 2021 |
| Contact name |
Jesse R Dixon |
| E-mail(s) |
jedixon@salk.edu
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| Organization name |
Salk Institute for Biological Studies
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| Lab |
PBL-D
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| Street address |
10010 N. Torrey Pines Rd.
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| City |
La Jolla |
| State/province |
CA |
| ZIP/Postal code |
92037 |
| Country |
USA |
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| Platforms (2) |
| GPL11154 |
Illumina HiSeq 2000 (Homo sapiens) |
| GPL16791 |
Illumina HiSeq 2500 (Homo sapiens) |
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| Samples (27)
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| GSM1267196 |
Hi-C, H1 embryonic stem cells, replicate one |
| GSM1267197 |
Hi-C, H1 embryonic stem cells, replicate two |
| GSM1267198 |
Hi-C, H1 Mesendoderm cells, replicate one |
| GSM1267199 |
Hi-C, H1 Mesendoderm cells, replicate two |
| GSM1267200 |
Hi-C, H1 Mesenchymal stem cells, replicate one |
| GSM1267201 |
Hi-C, H1 Mesenchymal stem cells, replicate two |
| GSM1267202 |
Hi-C, H1 Neuronal Progenitor cells, replicate one |
| GSM1267203 |
Hi-C, H1 Neuronal Progenitor cells, replicate two |
| GSM1267204 |
Hi-C, H1 Trophectoderm cells, replicate one |
| GSM1267205 |
Hi-C, H1 Trophectoderm cells, replicate two |
| GSM1267206 |
CTCF CHIP-Seq, H1 embryonic stem cells, replicate one |
| GSM1267207 |
CTCF CHIP-Seq, H1 Mesendoderm cells, replicate one |
| GSM1267208 |
CTCF CHIP-Seq, H1 Mesenchymal stem cells, replicate one |
| GSM1267209 |
CTCF CHIP-Seq, H1 Neuronal Progenitor cells, replicate one |
| GSM1267210 |
CTCF CHIP-Seq, H1 Trophectoderm cells, replicate one |
| GSM1412879 |
4C-seq, FAM65B bait, H1 embryonic stem cells, replicate one |
| GSM1412880 |
4C-seq, FAM65B bait, H1 embryonic stem cells, replicate two |
| GSM1412881 |
4C-seq, MT2A bait, H1 embryonic stem cells, replicate one |
| GSM1412882 |
4C-seq, MT2A bait, H1 embryonic stem cells, replicate two |
| GSM1412883 |
4C-seq, HAPLN1 bait, H1 mesenchymal stem cells, replicate one |
| GSM1412884 |
4C-seq, HAPLN1 bait, H1 mesenchymal stem cells, replicate two |
| GSM1412885 |
4C-seq, PXK bait, H1 mesenchymal stem cells, replicate one |
| GSM1412886 |
4C-seq, PXK bait, H1 mesenchymal stem cells, replicate two |
| GSM1412887 |
4C-seq, MAN1C1 bait, H1 mesenchymal stem cells, replicate one |
| GSM1412888 |
4C-seq, MAN1C1 bait, H1 mesenchymal stem cells, replicate two |
| GSM1412889 |
4C-seq, GCLM bait, H1 mesenchymal stem cells, replicate one |
| GSM1412890 |
4C-seq, GCLM bait, H1 mesenchymal stem cells, replicate two |
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| Relations |
| BioProject |
PRJNA228983 |
| SRA |
SRP033089 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE52457_BED_files.tar.gz |
7.3 Gb |
(ftp)(http) |
TAR |
| GSE52457_H1_haps.vcf.gz |
22.3 Mb |
(ftp)(http) |
VCF |
| GSE52457_RAW.tar |
280.0 Kb |
(http)(custom) |
TAR (of BEDGRAPH) |
| GSE52457_inference_files.tar.gz |
22.3 Mb |
(ftp)(http) |
TAR |
| GSE52457_reanalyzed_data_detail.xls.gz |
8.4 Kb |
(ftp)(http) |
XLS |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
| Processed data provided as supplementary file |
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