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Series GSE77565 Query DataSets for GSE77565
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.
 
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).*
 
Contributor(s) Geschwind DH, Won H
Citation(s) 27760116, 31160561
BioProject PRJNA304334
Submission date Feb 03, 2016
Last update date Jun 24, 2019
Contact name Hyejung Won
E-mail(s) wonhyejung87@gmail.com
Phone 3106000592
Organization name UCLA
Department Neurology
Street address 695 Charles E. Young Dr. South, Gonda 2309
City Los Angeles
State/province California
ZIP/Postal code 90095
Country USA
 
Platforms (1)
GPL11154 Illumina HiSeq 2000 (Homo sapiens)
Samples (6)
GSM2054564 CP, individual 1
GSM2054565 CP, individual 2
GSM2054566 CP, individual 3
Relations
SRA SRP066745

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

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
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Raw data are available in SRA
Processed data is available on Series record

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