GEO series

CTCF-RNA interactions orchestrate cell-specific chromatin loop organization [RNA-seq]

GSE287379 Mus musculus (mouse) RNA-seq (gene expression) 26 samples Submitted 2025/03/19 Platform GPL34328Platform GPL24247

At a glance

RNA-seq (gene expression) · mouse · 26 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: 26 samples: 10 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: CTCF-RNA interactions orchestrate cell-specific chromatin loop organizationbioRxiv : the preprint server for biology · 2025

Summary (written by the submitters)

CCCTC-binding factor (CTCF) is essential for chromatin organization, but its role in dynamically shaping chromatin loops during cellular differentiation is not fully understood. We previously demonstrated that CTCF interacts with endogenous RNAs, and deletion of its ZF1 RNA-binding region disrupts chromatin loops in mouse embryonic stem cells (ESCs).

Read the full summary ↓

Using an ESC-to-neural progenitor cell (NPC) differentiation model, we show that the ZF1 RNA-binding region of CTCF is crucial for maintaining cell-type specific chromatin loops. Expression of CTCF-∆ZF1 leads to dysregulation of genes within these disrupted loops, particularly those involved in neuronal development and function. We identified NPC-specific, CTCF-interacting RNAs and chose Podxl and Grb10 for further study. We found that CRISPR-Cas9-mediated truncation of Podxl and Grb10 disrupts chromatin loops in cis, similar to the disruption seen in the NPC-∆ZF1 mutant. Our study underscores the importance of CTCF-ZF1 RNA interactions in preserving cell-specific genome structure and cellular identity.

Published in

CTCF-RNA interactions orchestrate cell-specific chromatin loop organization

Lucero K, Han S, Huang PY et al. · bioRxiv : the preprint server for biology 2025 · PMID 40166279 · doi:10.1101/2025.03.19.643339

This dataset

Open GSE287379 in finder → Find more mouse 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 GSE287379_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: 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 PRJNA1212521 and SRA study SRP558250. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40166279) ↗

Study design

10 conditions, mostly in triplicate

RNA-seq_ESC, E14 WT, ×3 RNA-seq_ESC, Podxl SV40pA RNA truncation muta… ×3 RNA-seq_ESC, Grb10 SV40pA RNA truncation muta… ×3 RNA-seq_NPC, E14 WT, ×3 RNA-seq_NPC, Podxl SV40pA RNA truncation muta… ×3 RNA-seq_NPC, Grb10 SV40pA RNA truncation muta… ×3 RNA-seq_ESC, CTCF-WT rescue, ×2 RNA-seq_ESC, CTCF-ZF1 mutant rescue, ×2 +2 more

Supports a case/control comparison: 16 samples read as cases, 6 as controls.

How we read this: 10 replicated groups read from 26 sample titles; they account for 26 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

GSM8745099 RNA-seq_ESC, CTCF-WT rescue, rep1 RNA-seq_ESC, CTCF-WT re…
GSM8745100 RNA-seq_ESC, CTCF-WT rescue, rep2 RNA-seq_ESC, CTCF-WT re…
GSM8745101 RNA-seq_ESC, CTCF-ZF1 mutant rescue, rep1 RNA-seq_ESC, CTCF-ZF1 m…
GSM8745102 RNA-seq_ESC, CTCF-ZF1 mutant rescue, rep2 RNA-seq_ESC, CTCF-ZF1 m…
GSM8745103 RNA-seq_NPC, CTCF-WT rescue, rep1 RNA-seq_NPC, CTCF-WT re…
GSM8745104 RNA-seq_NPC, CTCF-WT rescue, rep2 RNA-seq_NPC, CTCF-WT re…
GSM8745105 RNA-seq_NPC, CTCF-ZF1 mutant rescue, rep1 RNA-seq_NPC, CTCF-ZF1 m…
GSM8745106 RNA-seq_NPC, CTCF-ZF1 mutant rescue, rep2 RNA-seq_NPC, CTCF-ZF1 m…
GSM8745107 RNA-seq_ESC, E14 WT, rep1 RNA-seq_ESC, E14 WT,
GSM8745108 RNA-seq_ESC, E14 WT, rep2 RNA-seq_ESC, E14 WT,
GSM8745109 RNA-seq_ESC, E14 WT, rep3 RNA-seq_ESC, E14 WT,
GSM8745110 RNA-seq_ESC, Podxl SV40pA RNA truncation mutant, rep1 RNA-seq_ESC, Podxl SV40…
GSM8745111 RNA-seq_ESC, Podxl SV40pA RNA truncation mutant, rep2 RNA-seq_ESC, Podxl SV40…
GSM8745112 RNA-seq_ESC, Podxl SV40pA RNA truncation mutant, rep3 RNA-seq_ESC, Podxl SV40…
GSM8745113 RNA-seq_ESC, Grb10 SV40pA RNA truncation mutant, rep1 RNA-seq_ESC, Grb10 SV40…
GSM8745114 RNA-seq_ESC, Grb10 SV40pA RNA truncation mutant, rep2 RNA-seq_ESC, Grb10 SV40…
GSM8745115 RNA-seq_ESC, Grb10 SV40pA RNA truncation mutant, rep3 RNA-seq_ESC, Grb10 SV40…
GSM8745116 RNA-seq_NPC, E14 WT, rep1 RNA-seq_NPC, E14 WT,
GSM8745117 RNA-seq_NPC, E14 WT, rep2 RNA-seq_NPC, E14 WT,
GSM8745118 RNA-seq_NPC, E14 WT, rep3 RNA-seq_NPC, E14 WT,
GSM8745119 RNA-seq_NPC, Podxl SV40pA RNA truncation mutant, rep1 RNA-seq_NPC, Podxl SV40…
GSM8745120 RNA-seq_NPC, Podxl SV40pA RNA truncation mutant, rep2 RNA-seq_NPC, Podxl SV40…
GSM8745121 RNA-seq_NPC, Podxl SV40pA RNA truncation mutant, rep3 RNA-seq_NPC, Podxl SV40…
GSM8745122 RNA-seq_NPC, Grb10 SV40pA RNA truncation mutant, rep1 RNA-seq_NPC, Grb10 SV40…
GSM8745123 RNA-seq_NPC, Grb10 SV40pA RNA truncation mutant, rep2 RNA-seq_NPC, Grb10 SV40…
GSM8745124 RNA-seq_NPC, Grb10 SV40pA RNA truncation mutant, rep3 RNA-seq_NPC, Grb10 SV40…

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GSE270817 Regulation of the type I interferon response by chromatin organization (RNA-seq of HoxB8-FL pDC activation) 12 samples shares organization, chromatin, rna-seq
GSE279025 cGAS deficient mice display premature aging associated with loss of chromatin organization, derepression of LINE1 elements and induction of inflammation [RNA-seq] 11 samples shares organization, chromatin, rna-seq
GSE261412 Acute hormonal signaling-induced 3D chromatin loop reorganization controls adipocyte thermogenesis [ChIP-Seq mouse, H3K27ac, H3K4me3, H2AZ] 24 samples shares organization, chromatin, loop
GSE263738 Bi-directional immunosuppressive interactions between astrocytes and glioblastoma cells identified by barcoded viral tracing [Mouse Bulk RNA-Seq Dataset of Monocytes, T Cells and Astrocytes 63FG] 57 samples shares interactions, rna-seq
GSE287837 Forced expression of MSR repeat transcripts above a threshold limit breaks heterochromatin organization 36 samples shares organization, chromatin

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