Pivotal Role of the NuRD Complex in Remodeling Chromatin Environment and Maintaining Genome Architecture at CTCF Sites [mESC ChIP-seq]
ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 18 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
- Mus musculus (mouse)
- Samples
- 18 samples: 6 conditions, mostly in triplicateGroups 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
- NuRD-enabled CTCF-TET crosstalk orchestrates epigenome reprogramming and genome architectureMolecular cell · 2026
Read the full summary ↓
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.
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.
Supplementary files
The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE278193_RAW.tar (it can run to tens of gigabytes).
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 PRJNA1165919 and SRA study SRP535170. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 18 samples.
How we read this: 6 replicated groups read from 18 sample titles; they account for 18 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.
- GSM8541614 mESC_WT_INPUT_rep1 mESC_WT_INPUT
- GSM8541615 mESC_WT_INPUT_rep2 mESC_WT_INPUT
- GSM8541616 mESC_WT_INPUT_rep3 mESC_WT_INPUT
- GSM8541617 mESC_WT_IP_CTCF_rep1 mESC_WT_IP_CTCF
- GSM8541618 mESC_WT_IP_CTCF_rep2 mESC_WT_IP_CTCF
- GSM8541619 mESC_WT_IP_CTCF_rep3 mESC_WT_IP_CTCF
- GSM8541620 mESC_SKO_INPUT_rep1 mESC_SKO_INPUT
- GSM8541621 mESC_SKO_INPUT_rep2 mESC_SKO_INPUT
- GSM8541622 mESC_SKO_INPUT_rep3 mESC_SKO_INPUT
- GSM8541623 mESC_SKO_IP_CTCF_rep1 mESC_SKO_IP_CTCF
- GSM8541624 mESC_SKO_IP_CTCF_rep2 mESC_SKO_IP_CTCF
- GSM8541625 mESC_SKO_IP_CTCF_rep3 mESC_SKO_IP_CTCF
- GSM8541626 mESC_TKO_INPUT_rep1 mESC_TKO_INPUT
- GSM8541627 mESC_TKO_INPUT_rep2 mESC_TKO_INPUT
- GSM8541628 mESC_TKO_INPUT_rep3 mESC_TKO_INPUT
- GSM8541629 mESC_TKO_IP_CTCF_rep1 mESC_TKO_IP_CTCF
- GSM8541630 mESC_TKO_IP_CTCF_rep2 mESC_TKO_IP_CTCF
- GSM8541631 mESC_TKO_IP_CTCF_rep3 mESC_TKO_IP_CTCF
- GSE253691 Pivotal Role of the NuRD Complex in Remodeling Chromatin Environment and Maintaining Genome Architecture at CTCF Sites [mESC_d0246_RNA_Seq] 12 samples shares ctcf, architecture, environment, maintaining, remodeling, chromatin, pivotal
- GSE278338 ChIP-seq to measure binding of NIPBL/MAU2, RAD21, and CTCF in mouse embryonic stem cells and neural progenitor cells 50 samples shares ctcf, chip-seq
- GSE243710 Analysis of three-dimensional enhancer network regulated by CTCF in CD4+ T cells [ChIP-seq] 33 samples shares ctcf, chip-seq
- GSE234273 Systematic assessment of ISWI subunits reveals that NURF creates local accessibility for CTCF [ChIP-seq] 32 samples shares ctcf, chip-seq
- GSE274792 CTCF tunes gene expression in a loop-dependent and -independent manner [ChIP-Seq] 30 samples shares ctcf, chip-seq
- GSE72539 CTCF binding polarity determines chromatin looping [4C] 504 samples shares ctcf, chromatin
- GSE261221 Scaffolding element rewires genome architecture during differentiation at the Zfp608 locus (ChIP-Seq) 189 samples shares architecture, chip-seq
- GSE314913 FACT maintains nucleosomes around promoters and opposes to the spreading of chromatin factors, thereby playing a major role in chromatin architecture [CUT&TAG] 36 samples shares architecture, chromatin
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.