GEO series

Genome-wide chromosomal conformation elucidates regulatory relationships in human brain development and disease

GSE77565 Homo sapiens (human) Other 6 samples Submitted 2016/10/20 Platform GPL11154

At a glance

human · 6 samples

Organism: Homo sapiens (human)
Samples: 6 samples
Data you can get: A processed table (series matrix) and supplementary files from NCBI.

Summary (written by the submitters)

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.

Read the full summary ↓

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.

This dataset

Open GSE77565 in finder → Find more human datasets →

Download · which file do I need?

Direct links to NCBI, no account and no request form. Pick by what you want to do: take the small processed table to look, the supplementary files to re-analyse, or the original raw data to start over.

1 · Just have a look

Processed table

The series matrix: one table of values per sample as the submitters processed it. The smallest download, and it opens in Excel or R. Start here to see what the data look like.

Series matrix ↓

2 · Re-analyse it

Supplementary files

The count tables and other files the authors uploaded. Take only the samples you need.

All supplementary files ↗

3 · The original raw files

Whole study · RAW.tar

Everything the authors deposited as one archive (GSE77565_RAW.tar), including the raw array or instrument files. Can be large; the picker in step 2 takes just the samples you need.

Whole study · RAW.tar ↓

Also filed as BioProject PRJNA304334 and SRA study SRP066745. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 27760116) ↗

Samples in this study

The sample list for this study is not cached yet. Press Load samples and it will be fetched from NCBI.

+ 6 more — browse all 6 samples with per-sample file links →

Datasets on a similar topic

GSE230342 Chromatin conformation dynamics during CD4+ Tcell activation implicates autoimmune disease associated genes and regulatory elements (HiC) 6 samples shares conformation, regulatory
GSE311978 Downregulated transcription in chromosomal domains of midbrain dopamine neurons linked to schizophrenia. [RNA-Seq] 97 samples shares chromosomal, brain
GSE288996 Simultaneous single cell CRISPR, RNA, and ATAC-seq enables multiomic CRISPR screens to identify gene regulatory relationships 15 samples shares relationships, regulatory
GSE285157 Genome-wide maps of enhancer regulation connect risk variants to disease genes 16 samples shares genome-wide
GSE281238 Generalization of the sci-L3 method to achieve high-throughput linear amplification for replication template strand sequencing, genome conformation capture, and the joint profiling of RNA and chromatin accessibility 7 samples shares conformation
GSE142751 Genome-wide maps of chromatin state in 142 cancer cell lines [cell line] 855 samples shares genome-wide
GSE18700 Genome-wide DNA methylation profiling of Acute Myeloid Leukemia 352 samples shares genome-wide
GSE276544 MVA-based SARS-CoV-2 vaccine candidates encoding different spike protein conformations induce distinct early transcriptional responses which may impact subsequent adaptive immunity 305 samples shares conformation

Search all human datasets in GEO →

Share this dataset

Metadata from NCBI GEO, cached and refreshed periodically — the NCBI page above is authoritative. Downloads link straight to NCBI/ENA; nothing is proxied through BioTransfer.