GEO series
Non-coding structural variants identify a commonly affected regulatory region steering FOXG1 transcription in early neurodevelopment [CUT&Run]
GSE292881
Homo sapiens (human)
ChIP-seq / ATAC-seq (genome binding and open chromatin)
47 samples
Submitted 2026/03/16
Platform GPL24676
At a glance
ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 47 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
- 47 samples: 37 distinct titles, 10 of them repeatedGroups 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.
Summary (written by the submitters)
The FOXG1 transcription factor is a crucial regulator of embryonic brain development. Pathogenic FOXG1 variants cause FOXG1 syndrome. Although structural variants (SVs) in the non-coding region downstream of FOXG1 have been reported in 38 individuals with similar characteristics, the regulatory pathomechanisms remain unknown. We identified a de novo non-coding deletion in an individual with FOXG1 syndrome-like disorder, allowing us to delineate a ~124 kb commonly affected regulatory region (CARR).
Read the full summary ↓
By integrating epigenomics data, 3D chromatin interaction profiles (Hi-C, UMI-4C), and in vivo enhancer assays in zebrafish, we uncovered multiple regulatory elements within this CARR, including a neuronal enhancer cluster and a conserved boundary of the FOXG1-containing topologically associating domain (TAD). Hi-C analysis on case lymphoblastoid cells revealed increased interactions with the adjacent TAD. Moreover, sequential UMI-4C and CUT&RUN assays during neural progenitor cell (NPC) differentiation demonstrated dynamic activation of, and interaction with the enhancer cluster. Finally, CRISPR-Cas9 deletion of the enhancer cluster and TAD boundary in NPCs resulted in decreased FOXG1 transcription. We identified and characterized enhancer and architectural elements essential for proper FOXG1 transcription. Our findings provide new insights into chromatin architecture and gene regulation at the FOXG1 locus, improving SV interpretation in individuals with FOXG1 syndrome-like disorder.
This dataset
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.
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 GSE292881_RAW.tar (it can run to tens of gigabytes).
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.
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 PRJNA1241808 and SRA study SRP573001. Searching any of these in the dataset finder brings you back here.
Study design
37 distinct titles, 10 of them repeated
NPC differentiation, day0, replicate 1, H3K4me ×2
NPC differentiation, day0, replicate 2, H3K4me ×2
NPC differentiation, day4, replicate 1, H3K4me ×2
NPC differentiation, day4, replicate 2, H3K4me ×2
NPC differentiation, day6, replicate 1, H3K4me ×2
NPC differentiation, day6, replicate 2, H3K4me ×2
NPC differentiation, day8, replicate 1, H3K4me ×2
NPC differentiation, day8, replicate 2, H3K4me ×2
+2 more
How we read this: Read from 47 sample titles: 37 distinct titles with little repetition. 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
- GSM8867948 NPC differentiation, day0, replicate 1, H3K4me3
- GSM8867949 NPC differentiation, day0, replicate 1, H3K4me1
- GSM8867950 NPC differentiation, day0, replicate 1, H3K27ac
- GSM8867951 NPC differentiation, day0, replicate 1, input
- GSM8867952 NPC differentiation, day0, replicate 2, H3K4me3
- GSM8867953 NPC differentiation, day0, replicate 2, H3K4me1
- GSM8867954 NPC differentiation, day0, replicate 2, H3K27ac
- GSM8867955 NPC differentiation, day0, replicate 2, input
- GSM8867956 NPC differentiation, day4, replicate 1, H3K4me3
- GSM8867957 NPC differentiation, day4, replicate 1, H3K4me1
- GSM8867958 NPC differentiation, day4, replicate 1, H3K27ac
- GSM8867959 NPC differentiation, day4, replicate 1, input
- GSM8867960 NPC differentiation, day4, replicate 2, H3K4me3
- GSM8867961 NPC differentiation, day4, replicate 2, H3K4me1
- GSM8867962 NPC differentiation, day4, replicate 2, H3K27ac
- GSM8867963 NPC differentiation, day4, replicate 2, input
- GSM8867964 NPC differentiation, day6, replicate 1, H3K4me3
- GSM8867965 NPC differentiation, day6, replicate 1, H3K4me1
- GSM8867966 NPC differentiation, day6, replicate 1, H3K27ac
- GSM8867967 NPC differentiation, day6, replicate 1, input
- GSM8867968 NPC differentiation, day6, replicate 2, H3K4me3
- GSM8867969 NPC differentiation, day6, replicate 2, H3K4me1
- GSM8867970 NPC differentiation, day6, replicate 2, H3K27ac
- GSM8867971 NPC differentiation, day6, replicate 2, input
- GSM8867972 NPC differentiation, day8, replicate 1, H3K4me3
- GSM8867973 NPC differentiation, day8, replicate 1, H3K4me1
- GSM8867974 NPC differentiation, day8, replicate 1, H3K27ac
- GSM8867975 NPC differentiation, day8, replicate 1, input
- GSM8867976 NPC differentiation, day8, replicate 2, H3K4me3
- GSM8867977 NPC differentiation, day8, replicate 2, H3K4me1
- GSM8867978 NPC differentiation, day8, replicate 2, H3K27ac
- GSM8867979 NPC differentiation, day8, replicate 2, input
- GSM9575741 forebrain NPC differentiation, day 14, replicate 1, H3K4me3
- GSM9575742 forebrain NPC differentiation, day 14, replicate 1, H3K4me1
- GSM9575743 forebrain NPC differentiation, day 14, replicate 1, H3K27ac
- GSM9575744 forebrain NPC differentiation, day 14, replicate 1, CTCF
- GSM9575745 forebrain NPC differentiation, day 14, replicate 1, input
- GSM9575746 forebrain NPC differentiation, day 14, replicate 2, H3K4me3
- GSM9575747 forebrain NPC differentiation, day 14, replicate 2, H3K4me1
- GSM9575748 forebrain NPC differentiation, day 14, replicate 2, H3K27ac
+ 7 more — browse all 47 samples with per-sample file links →
Datasets on a similar topic
- GSE294275 Transcriptional analysis of direct NSD2 target genes in t(4;14) multiple myeloma reveals H3K36me2-dependent regulation and H3K27me3 antagonism [CUT&TAG] 40 samples shares cut, transcription
- GSE291224 AF9/KLF2 gene regulatory circuit links histone lactylation to breast cancer metastasis [CUT&Tag] 22 samples shares cut, regulatory
- GSE267470 Dual targeting of processive transcription for Myc-driven circuitry in medulloblastoma [CUT&RUN] 12 samples shares cut, transcription
- GSE178411 Whole-transcriptome analysis illustrates evolving transcriptional human response to injury in acute wounds and scars 108 samples shares cut, transcription
- GSE270503 Epigenetic heterogeneity and state-specific transcriptional programs determine differential drug response in osteosarcoma [Cut&Run] 56 samples shares cut, transcription
- GSE302930 Epigenetic Atlas of Bladder Cancer Reveals Master Transcription Factors and Risk-Associated Regulatory Elements in Luminal and Basal-Squamous Molecular Subtypes 92 samples shares transcription, regulatory
- GSE327821 Single-molecule, single-cell profiling of linked chromatin states [Single_cell_CoCUT&Tag] 200 samples shares cut
- GSE339365 Genome-wide H3K4me3 profiling of circulating immune cells reveals dynamic epigenetic reprogramming during acute critical COVID-19 120 samples shares cut
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.