|
| Status |
Public on Jun 26, 2020 |
| Title |
Robust Hi-C maps of enhancer-promoter interactions reveal the function of non-coding genome in neural development and diseases |
| Organism |
Homo sapiens |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
Other
Third-party reanalysis
Expression profiling by high throughput sequencing
|
| Summary |
Despite recent progress in mammalian 3D genome studies, it remains experimentally and computationally challenging to identify chromatin interactions genome-wide. Here we developed a highly efficient “easy Hi-C” (eHi-C) protocol that generates high-yield libraries with 0.1 million cells. After rigorous bias-correction with a significantly improved Hi-C analysis pipeline, we can directly recognize the dynamic long- and short-range chromatin loops from contact heatmaps. We compared 10 ultra-deep Hi-C or eHi-C datasets (billion- read scale) from human tissue- or cell types focusing on brain and neurogenesis. We found that H3K9me3 marks a 3D genome compartmental barrier for induced pluripotency. Dynamic chromatin loops, but not genome compartments, are hallmarks of neuronal differentiation and neuron-related diseases. Interestingly, we observed many neuron-specific enhancer-promoter looping clusters spanning Mb-scale neighborhoods, supporting a phase-separation model leading to enhancer aggregation during brain development. Taken together, our 3D genome analyses shed light on the regulation of brain development and complex neuronal diseases.
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| |
|
| Overall design |
3D genome structure mapping in human neurogenesis (from human induced pluripiotent stem cells to neural progenitor cells to neuron cells) using a newly designed easy Hi-C method
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GSM1267196: anchor_2_anchor.loop.H1.txt.gz
GSM1267197: anchor_2_anchor.loop.H1.txt.gz
GSM1055800: anchor_2_anchor.loop.IMR90.txt.gz
GSM1055801: anchor_2_anchor.loop.IMR90.txt.gz
GSM1154021: anchor_2_anchor.loop.IMR90.txt.gz
GSM1154022: anchor_2_anchor.loop.IMR90.txt.gz
GSM1154023: anchor_2_anchor.loop.IMR90.txt.gz
GSM1154024: anchor_2_anchor.loop.IMR90.txt.gz
GSM1055802: anchor_2_anchor.loop.IMR90.txt.gz
GSM1055803: anchor_2_anchor.loop.IMR90.txt.gz
GSM1154025: anchor_2_anchor.loop.IMR90.txt.gz
GSM1154026: anchor_2_anchor.loop.IMR90.txt.gz
GSM1154027: anchor_2_anchor.loop.IMR90.txt.gz
GSM1154028: anchor_2_anchor.loop.IMR90.txt.gz
GSM1181867: anchor_2_anchor.loop.GM12878.txt.gz
GSM1181868: anchor_2_anchor.loop.GM12878.txt.gz
GSM1551583: anchor_2_anchor.loop.GM12878.txt.gz
GSM1551584: anchor_2_anchor.loop.GM12878.txt.gz
GSM1551586: anchor_2_anchor.loop.GM12878.txt.gz
GSM1608505: anchor_2_anchor.loop.GM12878.txt.gz
GSM2054564: anchor_2_anchor.loop.CP.txt.gz
GSM2054565: anchor_2_anchor.loop.CP.txt.gz
GSM2054566: anchor_2_anchor.loop.CP.txt.gz
GSM2054567: anchor_2_anchor.loop.GZ.txt.gz
GSM2054568: anchor_2_anchor.loop.GZ.txt.gz
GSM2054569: anchor_2_anchor.loop.GZ.txt.gz
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| |
|
| Contributor(s) |
Lu L, Liu X, Huang W, Li Y, Jin F, Ming G |
| Citation(s) |
32592681 |
| |
| Submission date |
Jun 06, 2018 |
| Last update date |
Feb 22, 2021 |
| Contact name |
Xiaoxiao Liu |
| E-mail(s) |
[email protected]
|
| Phone |
(216) 368-5293
|
| Organization name |
Case Western Reserve University
|
| Department |
Genetics and Genomes Sciences
|
| Lab |
Fulai Jin
|
| Street address |
10900 Euclid Ave
|
| City |
Cleveland |
| State/province |
Ohio |
| ZIP/Postal code |
44120 |
| Country |
USA |
| |
|
| Platforms (3) |
| GPL16791 |
Illumina HiSeq 2500 (Homo sapiens) |
| GPL20301 |
Illumina HiSeq 4000 (Homo sapiens) |
| GPL20795 |
HiSeq X Ten (Homo sapiens) |
|
| Samples (40)
|
|
| Relations |
| Reanalysis of |
GSM1267196 |
| Reanalysis of |
GSM1267197 |
| Reanalysis of |
GSM1055800 |
| Reanalysis of |
GSM1055801 |
| Reanalysis of |
GSM1154021 |
| Reanalysis of |
GSM1154022 |
| Reanalysis of |
GSM1154023 |
| Reanalysis of |
GSM1154024 |
| Reanalysis of |
GSM1055802 |
| Reanalysis of |
GSM1055803 |
| Reanalysis of |
GSM1154025 |
| Reanalysis of |
GSM1154026 |
| Reanalysis of |
GSM1154027 |
| Reanalysis of |
GSM1154028 |
| Reanalysis of |
GSM1181867 |
| Reanalysis of |
GSM1181868 |
| Reanalysis of |
GSM1551583 |
| Reanalysis of |
GSM1551584 |
| Reanalysis of |
GSM1551586 |
| Reanalysis of |
GSM1608505 |
| Reanalysis of |
GSM2054564 |
| Reanalysis of |
GSM2054565 |
| Reanalysis of |
GSM2054566 |
| Reanalysis of |
GSM2054567 |
| Reanalysis of |
GSM2054568 |
| Reanalysis of |
GSM2054569 |
| BioProject |
PRJNA474896 |
| SRA |
SRP149906 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE115407_CP.loops.txt.gz |
3.6 Mb |
(ftp)(http) |
TXT |
| GSE115407_GM12878.loops.txt.gz |
3.4 Mb |
(ftp)(http) |
TXT |
| GSE115407_GM12878_CTCF_peaks.bed.gz |
566.9 Kb |
(ftp)(http) |
BED |
| GSE115407_GM12878_H3K27ac_peaks.bed.gz |
557.3 Kb |
(ftp)(http) |
BED |
| GSE115407_GM12878_H3K27me3_peaks.bed.gz |
52.3 Kb |
(ftp)(http) |
BED |
| GSE115407_GM12878_H3K36me3_peaks.bed.gz |
537.1 Kb |
(ftp)(http) |
BED |
| GSE115407_GM12878_H3K4me1_peaks.bed.gz |
770.0 Kb |
(ftp)(http) |
BED |
| GSE115407_GM12878_H3K4me3_peaks.bed.gz |
587.7 Kb |
(ftp)(http) |
BED |
| GSE115407_GM12878_H3K9me3_peaks.bed.gz |
270.0 Kb |
(ftp)(http) |
BED |
| GSE115407_GZ.loops.txt.gz |
3.5 Mb |
(ftp)(http) |
TXT |
| GSE115407_H1.loops.txt.gz |
3.6 Mb |
(ftp)(http) |
TXT |
| GSE115407_H1_CTCF_peaks.bed.gz |
1.3 Mb |
(ftp)(http) |
BED |
| GSE115407_H1_H3K27ac_peaks.bed.gz |
1.2 Mb |
(ftp)(http) |
BED |
| GSE115407_H1_H3K27me3_peaks.bed.gz |
530.0 Kb |
(ftp)(http) |
BED |
| GSE115407_H1_H3K36me3_peaks.bed.gz |
1.5 Mb |
(ftp)(http) |
BED |
| GSE115407_H1_H3K4me1_peaks.bed.gz |
2.9 Mb |
(ftp)(http) |
BED |
| GSE115407_H1_H3K4me3_peaks.bed.gz |
372.1 Kb |
(ftp)(http) |
BED |
| GSE115407_H1_H3K9me3_peaks.bed.gz |
2.0 Mb |
(ftp)(http) |
BED |
| GSE115407_IMR90.loops.txt.gz |
3.6 Mb |
(ftp)(http) |
TXT |
| GSE115407_IMR90_CTCF_peaks.bed.gz |
643.4 Kb |
(ftp)(http) |
BED |
| GSE115407_IMR90_H3K27ac_peaks.bed.gz |
807.6 Kb |
(ftp)(http) |
BED |
| GSE115407_IMR90_H3K27me3_peaks.bed.gz |
949.5 Kb |
(ftp)(http) |
BED |
| GSE115407_IMR90_H3K36me3_peaks.bed.gz |
1.4 Mb |
(ftp)(http) |
BED |
| GSE115407_IMR90_H3K4me1_peaks.bed.gz |
1.4 Mb |
(ftp)(http) |
BED |
| GSE115407_IMR90_H3K4me3_peaks.bed.gz |
288.8 Kb |
(ftp)(http) |
BED |
| GSE115407_IMR90_H3K9me3_peaks.bed.gz |
251.8 Kb |
(ftp)(http) |
BED |
| GSE115407_RAW.tar |
4.0 Gb |
(http)(custom) |
TAR (of BED, TXT) |
| GSE115407_RNAseq_Complete_geneList_EdgeR.xlsx |
16.4 Mb |
(ftp)(http) |
XLSX |
| GSE115407_anchor_2_anchor.loop.CP.txt.gz |
1.3 Gb |
(ftp)(http) |
TXT |
| GSE115407_anchor_2_anchor.loop.GM12878.txt.gz |
1.5 Gb |
(ftp)(http) |
TXT |
| GSE115407_anchor_2_anchor.loop.GZ.txt.gz |
1.4 Gb |
(ftp)(http) |
TXT |
| GSE115407_anchor_2_anchor.loop.H1.txt.gz |
1.3 Gb |
(ftp)(http) |
TXT |
| GSE115407_anchor_2_anchor.loop.IMR90.txt.gz |
1.4 Gb |
(ftp)(http) |
TXT |
| GSE115407_anchor_2_anchor.loop.cortex_adult.txt.gz |
1.4 Gb |
(ftp)(http) |
TXT |
| GSE115407_anchor_2_anchor.loop.cortex_fetal.txt.gz |
1.4 Gb |
(ftp)(http) |
TXT |
| GSE115407_cortex_adult.loops.txt.gz |
3.0 Mb |
(ftp)(http) |
TXT |
| GSE115407_cortex_fetal.loops.txt.gz |
2.1 Mb |
(ftp)(http) |
TXT |
| GSE115407_hiPSC_1011.frag_loop.txt.gz |
689.7 Mb |
(ftp)(http) |
TXT |
| GSE115407_hiPSC_1019.frag_loop.txt.gz |
766.7 Mb |
(ftp)(http) |
TXT |
| GSE115407_hiPSC_1026.frag_loop.txt.gz |
748.8 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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