|
| Status |
Public on Oct 20, 2016 |
| Title |
Genome-wide chromosomal conformation elucidates regulatory relationships in human brain development and disease |
| Organism |
Homo sapiens |
| Experiment type |
Other
|
| Summary |
The demonstration that chromatin exhibits a complex 3 dimensional organization, whereby short and long distance physical interactions correspond to complex gene regulatory processes has opened a new window on understanding the functional organization of the human genome. Recently, chromatin remodeling has also been causally implicated in several neurodevelopmental disorders, including autism and schizophrenia. However, it remains unclear whether knowledge of chromosome organization in a tissue specific manner might inform our understanding of gene regulation in brain development or disease. Here we determined the genome-wide landscape of chromosome conformation during early human cortical development by performing Hi-C analysis in the mitotically active and post mitotic laminae of human fetal brain. We integrate Hi-C data with transcriptomic and epigenomic data and utilize chromosome contact information to delineate physical gene-gene regulatory interactions for non-coding regulatory elements. We show how these data permit large-scale functional annotation of non-coding variants identified in schizophrenia GWAS and of human specific enhancers. These data provide a rubric that illustrates the power of tissue-specific annotation of non-coding regulatory elements, as well as novel insights into the pathogenic mechanisms of neurodevelopmental disorders and the evolution of higher cognition.
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| |
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| Overall design |
Hi-C data of fetal cortical anlage from three individuals. SRA: SRP066745, BioProject ID: PRJNA304334, dbGaP: phs001190.v1.p1.
*Raw reads are available through dbGaP (phs001190.v1.p1).*
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| |
|
| Contributor(s) |
Geschwind DH, Won H |
| Citation(s) |
27760116, 31160561 |
| BioProject |
PRJNA304334 |
| |
| Submission date |
Feb 03, 2016 |
| Last update date |
Feb 22, 2021 |
| Contact name |
Hyejung Won |
| E-mail(s) |
hyejung_won@med.unc.edu
|
| Phone |
3106000592
|
| Organization name |
UNC
|
| Department |
Genetics
|
| Street address |
116 Manning Dr.
|
| City |
Chapel Hill |
| State/province |
North Carolina |
| ZIP/Postal code |
27599 |
| Country |
USA |
| |
|
| Platforms (1) |
| GPL11154 |
Illumina HiSeq 2000 (Homo sapiens) |
|
| Samples (6)
|
|
| Relations |
| SRA |
SRP066745 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE77565_CP_TAD.bed.gz |
12.5 Kb |
(ftp)(http) |
BED |
| GSE77565_Evolloci_interacting_region_enhctrl_ES_FDR.bed.gz |
91.4 Kb |
(ftp)(http) |
BED |
| GSE77565_Evolloci_interacting_region_enhctrl_FBD1_FDR.bed.gz |
58.8 Kb |
(ftp)(http) |
BED |
| GSE77565_Evolloci_interacting_region_enhctrl_FBD2_FDR.bed.gz |
64.0 Kb |
(ftp)(http) |
BED |
| GSE77565_Evolloci_interacting_region_enhctrl_FBD3_FDR.bed.gz |
64.1 Kb |
(ftp)(http) |
BED |
| GSE77565_Evolloci_interacting_region_enhctrl_FBD_FDR.bed.gz |
92.5 Kb |
(ftp)(http) |
BED |
| GSE77565_Evolloci_interacting_region_enhctrl_FBP1_FDR.bed.gz |
57.3 Kb |
(ftp)(http) |
BED |
| GSE77565_Evolloci_interacting_region_enhctrl_FBP2_FDR.bed.gz |
61.8 Kb |
(ftp)(http) |
BED |
| GSE77565_Evolloci_interacting_region_enhctrl_FBP3_FDR.bed.gz |
70.6 Kb |
(ftp)(http) |
BED |
| GSE77565_Evolloci_interacting_region_enhctrl_FBP_FDR.bed.gz |
93.6 Kb |
(ftp)(http) |
BED |
| GSE77565_Evolloci_interacting_region_enhctrl_IMR90_FDR.bed.gz |
52.2 Kb |
(ftp)(http) |
BED |
| GSE77565_FBD_IC-heatmap-chr-10k.hdf5.gz |
4.6 Gb |
(ftp)(http) |
HDF5 |
| GSE77565_FBD_IC-heatmap-chr-40k.hdf5.gz |
1.1 Gb |
(ftp)(http) |
HDF5 |
| GSE77565_FBD_IC-heatmap-res-100k.hdf5.gz |
4.1 Gb |
(ftp)(http) |
HDF5 |
| GSE77565_FBP_IC-heatmap-chr-10k.hdf5.gz |
4.8 Gb |
(ftp)(http) |
HDF5 |
| GSE77565_FBP_IC-heatmap-chr-40k.hdf5.gz |
1.2 Gb |
(ftp)(http) |
HDF5 |
| GSE77565_FBP_IC-heatmap-res-100k.hdf5.gz |
4.2 Gb |
(ftp)(http) |
HDF5 |
| GSE77565_GZ_TAD.bed.gz |
13.3 Kb |
(ftp)(http) |
BED |
| GSE77565_Sczloci_interacting_region_ES_FDR.bed.gz |
27.1 Kb |
(ftp)(http) |
BED |
| GSE77565_Sczloci_interacting_region_FBD1_FDR.bed.gz |
21.9 Kb |
(ftp)(http) |
BED |
| GSE77565_Sczloci_interacting_region_FBD2_FDR.bed.gz |
24.1 Kb |
(ftp)(http) |
BED |
| GSE77565_Sczloci_interacting_region_FBD3_FDR.bed.gz |
23.3 Kb |
(ftp)(http) |
BED |
| GSE77565_Sczloci_interacting_region_FBD_FDR.bed.gz |
40.4 Kb |
(ftp)(http) |
BED |
| GSE77565_Sczloci_interacting_region_FBP1_FDR.bed.gz |
20.1 Kb |
(ftp)(http) |
BED |
| GSE77565_Sczloci_interacting_region_FBP2_FDR.bed.gz |
23.2 Kb |
(ftp)(http) |
BED |
| GSE77565_Sczloci_interacting_region_FBP3_FDR.bed.gz |
27.6 Kb |
(ftp)(http) |
BED |
| GSE77565_Sczloci_interacting_region_FBP_FDR.bed.gz |
37.0 Kb |
(ftp)(http) |
BED |
| GSE77565_Sczloci_interacting_region_IMR90_FDR.bed.gz |
16.8 Kb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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