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Loss of extreme long-range enhancers in human neural crest drives a craniofacial disorder

GSE145327 Homo sapiens (human) ChIP-seq / ATAC-seq (genome binding and open chromatin) 80 samples Submitted 2020/09/28 Platform GPL20301Platform GPL18573
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 80 samples

What it is
ChIP-seq / ATAC-seq (genome binding and open chromatin)Where proteins bind the genome, or which regions are open and active.
Organism
Homo sapiens (human)
Samples
80 samples: 19 conditions, mostly with about 4 replicates eachGroups are read from the sample names, not from the paper. Check the list below.
Data you can get
A processed table (series matrix) and supplementary files from NCBI; the raw sequencing reads from ENA. Which of these hold counts depends on the study, so check the file list.
Paper
Loss of Extreme Long-Range Enhancers in Human Neural Crest Drives a Craniofacial DisorderCell stem cell · 2020
Summary (written by the submitters)
Non-coding mutations at the far end of a large gene desert surrounding the SOX9 gene result in a human craniofacial disorder called Pierre Robin sequence (PRS). In this study we utilise epigenomic profiling of histone modifications and coactivator binding using ChIP-seq and chromatin accessibility using ATAC-seq to map cis-regulatory enhancer elements within the PRS locus during differentiation of human embryonic stem cells to cranial neural crest and chondrocytes.
Read the full summary ↓
Strikingly, these enhancers are located up to 1.45 Mb away from the SOX9 gene promoter. We further perform RNA-sequencing to determine gene expression changes during the differentiation and identify potential transcription factors that regulate enhancer activity during CNCC development, including TWIST1. We utilise Capture-C from the SOX9 promoter to profile long-range interactions with the distal PRS-associated enhancer elements, and we confirm these interactions using reciprocal Capture-C from the identified candidate enhancer elements. Finally, we phase the H9 human embryonic stem cell line using 10X genomics linked-read sequencing in order link genetically edited alleles to gene expresssion changes in cis. Overall, we characterize the longest-range human enhancers involved in congenital malformations, directly demonstrate that PRS is an enhanceropathy, and identify one factor that may contribute to enhancer function in a developmentally-regulated manner.
Published in
Loss of Extreme Long-Range Enhancers in Human Neural Crest Drives a Craniofacial Disorder
Long HK, Osterwalder M, Welsh IC et al. · Cell stem cell 2020 · PMID 32991838 · doi:10.1016/j.stem.2020.09.001
This dataset
Open GSE145327 in finder → Find more human RNA-seq datasets →
Download · which file do I need?

Direct links to NCBI and ENA, 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, or the whole study as GSE145327_RAW.tar (it can run to tens of gigabytes).

All supplementary files ↗ Whole study · RAW.tar ↓
3 · Start from the raw reads

Raw sequencing reads

The original FASTQ files, straight from the sequencer, held at ENA. Large, and you align them yourself, so only choose this if you need to re-process the study from scratch.

Raw reads on ENA ↗

What the files usually look like: Look for peak files (.bed, .narrowPeak) and signal tracks (.bigWig) among the supplementary files; the raw reads are on ENA.

Also filed as BioProject PRJNA606766 and SRA study SRP249553. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 32991838) ↗
Study design
19 conditions, mostly with about 4 replicates each
H9_ESC_ATACseq ×4 H9_P2CNCC_ATACseq ×4 H9_P4CNCC_ATACseq ×4 H9_Day9chond_ATACseq ×4 H9_ESC_RNAseq ×4 H9_P1CNCC_RNAseq ×4 H9_P2CNCC_RNAseq ×4 H9_P3CNCC_RNAseq ×4 +32 more

Supports a between-group comparison across 59 samples.

How we read this: 19 replicated groups read from 80 sample titles; they account for 59 of them. These groups are guessed from the sample names, not taken from the paper, so check them against the sample list below before relying on them.

Samples in this study

+ 40 more — browse all 80 samples with per-sample file links →

Datasets on a similar topic

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