Pivotal Role of the NuRD Complex in Remodeling Chromatin Environment and Maintaining Genome Architecture at CTCF Sites [mESC_d0246_RNA_Seq]
RNA-seq (gene expression) · mouse · 12 samples
- What it is
- RNA-seq (gene expression)Gene activity measured by sequencing. The summary does not mention single-cell work, so this is most likely bulk: one average per sample, the usual starting point for comparing groups.
- Organism
- Mus musculus (mouse)
- Samples
- 12 samples: 3 × mESC_d0 vs 3 × mESC_d2 vs 3 × mESC_d4 vs 3 × mESC_d6Groups 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 GSE253691_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: For RNA-seq the counts are usually a table among the supplementary files (look for 'counts', 'expression', 'FPKM' or 'TPM' in the file name). The series matrix of a sequencing study is sometimes nearly empty.
Also filed as BioProject PRJNA1066779 and SRA study SRP484820. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 12 samples.
How we read this: 4 replicated groups read from 12 sample titles; they account for 12 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.
- GSM8026413 mESC_d0_rep1 mESC_d0
- GSM8026414 mESC_d0_rep2 mESC_d0
- GSM8026415 mESC_d0_rep3 mESC_d0
- GSM8026416 mESC_d2_rep1 mESC_d2
- GSM8026417 mESC_d2_rep2 mESC_d2
- GSM8026418 mESC_d2_rep3 mESC_d2
- GSM8026419 mESC_d4_rep1 mESC_d4
- GSM8026420 mESC_d4_rep2 mESC_d4
- GSM8026421 mESC_d4_rep3 mESC_d4
- GSM8026422 mESC_d6_rep1 mESC_d6
- GSM8026423 mESC_d6_rep2 mESC_d6
- GSM8026424 mESC_d6_rep3 mESC_d6
- GSE253693 Pivotal Role of the NuRD Complex in Remodeling Chromatin Environment and Maintaining Genome Architecture at CTCF Sites [mESC_d0246_DMSO_BPK25_IAA_RNA_Seq] 36 samples shares d0246, ctcf, architecture, environment, maintaining, remodeling, chromatin, pivotal
- GSE253692 Pivotal Role of the NuRD Complex in Remodeling Chromatin Environment and Maintaining Genome Architecture at CTCF Sites [mESC_d0246_CTCF_MBD3_ChIP_Seq] 36 samples shares d0246, ctcf, architecture, environment, maintaining, remodeling, chromatin, pivotal
- GSE72539 CTCF binding polarity determines chromatin looping [4C] 504 samples shares ctcf, chromatin
- GSE255858 O-GlcNAcylation of CTCF regulates 3D chromatin structure [HiC] 6 samples shares ctcf, chromatin
- GSE259380 TG6050, an oncolytic vaccinia virus encoding interleukin-12 and anti-CTLA-4 antibody induces tumor regression through profound tumor microenvironment remodeling and strong antitumor adaptive immune response [RNA-seq] 149 samples shares environment, remodeling
- GSE306986 Synergistic Stromal Remodeling and Dual Chemo-Immunotherapy in Pancreatic Cancer: A Two-Stage Losartan-Primed followed Nanocarrier Strategy for Tumor Microenvironment Reprogramming 24 samples shares environment, remodeling
- GSE319318 Inactivation of CDKN2A-ARF Promotes p53-Independent Remodeling of the PDAC Tumor Microenvironment [RNA-Seq] 20 samples shares environment, remodeling
- GSE309618 Mesangial cell-derived extracellular matrix protein 1 is essential for maintaining mesangial matrix homeostasis and glomerular architecture 18 samples shares architecture, maintaining
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.