GEO series
ChAHP Silences SINE Retrotransposons by Inhibiting TFIIIB Recruitment [RNA-seq]
GSE297833
Mus musculus (mouse)
RNA-seq (gene expression)
54 samples
Submitted 2026/05/01
Platform GPL24247
At a glance
RNA-seq (gene expression) · mouse · 54 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
- 54 samples: 18 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
- ChAHP silences SINE retrotransposons by inhibiting TFIIIB recruitmentMolecular cell · 2026
Summary (written by the submitters)
Short interspersed nuclear elements (SINEs) are abundant non-autonomous transposable elements (TEs) derived from RNA polymerase III (Pol III)-transcribed short non-coding RNAs. SINEs retain sequence features recognized by the Pol III machinery and constitute a substantial portion of vertebrate genomes. Despite their impact on genome stability and evolution, the mechanisms governing SINE transcription remain poorly understood.
Read the full summary ↓
Although DNA methylation and heterochromatin formation have been implicated in their repression, we find these pathways play only a minor role in mouse embryonic stem cells. Instead, we identify the ChAHP complex as a key repressor of SINE B2 elements. ChAHP directly inhibits Pol III transcription by blocking TFIIIB recruitment without affecting TFIIIC binding. This selective interference prevents transcription initiation and highlights a distinct regulatory mechanism. Our findings establish ChAHP as a non-canonical repressor of Pol III-dependent SINE transcription, offering new insights into the control of this pervasive class of non-coding genomic elements.
Published in
Schnabl-Baumgartner J, Mohn F, Schwaiger M et al.
· Molecular cell 2026
· PMID 42413492
· doi:10.1016/j.molcel.2026.06.024
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 GSE297833_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: 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 PRJNA1266249 and SRA study SRP587035. Searching any of these in the dataset finder brings you back here.
Study design
18 conditions, mostly in triplicate
RNA-seq in ADNP-FKBP12 mESC, ctrl, 1h, ×3
RNA-seq in ADNP-FKBP12 mESC, ctrl, 24h, ×3
RNA-seq in ADNP-FKBP12 mESC, ctrl, 4h, ×3
RNA-seq in ADNP-FKBP12 mESC, dTAG13, 24h, ×3
RNA-seq in ADNP-FKBP12 mESC, dTAG13, 4h, ×3
RNA-seq in ADNP-FKBP12 CTCF-FKBP12 mESC, ctrl… ×3
RNA-seq in ADNP-FKBP12 CTCF-FKBP12 mESC, dTAG… ×3
RNA-seq in CTCF-FKBP12 mESC, ctrl, 24h, ×3
+12 more
Supports a between-group comparison across 52 samples.
How we read this: 18 replicated groups read from 54 sample titles; they account for 52 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
- GSM9000627 RNA-seq in ADNP-FKBP12 mESC, ctrl, 1h, replicate 1 RNA-seq in ADNP-FKBP12 …
- GSM9000628 RNA-seq in ADNP-FKBP12 mESC, ctrl, 1h, replicate 2 RNA-seq in ADNP-FKBP12 …
- GSM9000629 RNA-seq in ADNP-FKBP12 mESC, ctrl, 1h, replicate 3 RNA-seq in ADNP-FKBP12 …
- GSM9000630 RNA-seq in ADNP-FKBP12 mESC, ctrl, 24h, replicate 1 RNA-seq in ADNP-FKBP12 …
- GSM9000631 RNA-seq in ADNP-FKBP12 mESC, ctrl, 24h, replicate 2 RNA-seq in ADNP-FKBP12 …
- GSM9000632 RNA-seq in ADNP-FKBP12 mESC, ctrl, 24h, replicate 3 RNA-seq in ADNP-FKBP12 …
- GSM9000633 RNA-seq in ADNP-FKBP12 mESC, ctrl, 4h, replicate 1 RNA-seq in ADNP-FKBP12 …
- GSM9000634 RNA-seq in ADNP-FKBP12 mESC, ctrl, 4h, replicate 2 RNA-seq in ADNP-FKBP12 …
- GSM9000635 RNA-seq in ADNP-FKBP12 mESC, ctrl, 4h, replicate 3 RNA-seq in ADNP-FKBP12 …
- GSM9000636 RNA-seq in ADNP-FKBP12 mESC, dTAG13, 1h, replicate 1
- GSM9000637 RNA-seq in ADNP-FKBP12 mESC, dTAG13, 1h, replicate 2 RNA-seq in ADNP-FKBP12 …
- GSM9000638 RNA-seq in ADNP-FKBP12 mESC, dTAG13, 1h, replicate 3 RNA-seq in ADNP-FKBP12 …
- GSM9000639 RNA-seq in ADNP-FKBP12 mESC, dTAG13, 24h, replicate 1 RNA-seq in ADNP-FKBP12 …
- GSM9000640 RNA-seq in ADNP-FKBP12 mESC, dTAG13, 24h, replicate 2 RNA-seq in ADNP-FKBP12 …
- GSM9000641 RNA-seq in ADNP-FKBP12 mESC, dTAG13, 24h, replicate 3 RNA-seq in ADNP-FKBP12 …
- GSM9000642 RNA-seq in ADNP-FKBP12 mESC, dTAG13, 4h, replicate 1 RNA-seq in ADNP-FKBP12 …
- GSM9000643 RNA-seq in ADNP-FKBP12 mESC, dTAG13, 4h, replicate 2 RNA-seq in ADNP-FKBP12 …
- GSM9000644 RNA-seq in ADNP-FKBP12 mESC, dTAG13, 4h, replicate 3 RNA-seq in ADNP-FKBP12 …
- GSM9000645 RNA-seq in ADNP-FKBP12 CTCF-FKBP12 mESC, ctrl, 24h, replicate 1 RNA-seq in ADNP-FKBP12 …
- GSM9000646 RNA-seq in ADNP-FKBP12 CTCF-FKBP12 mESC, ctrl, 24h, replicate 2 RNA-seq in ADNP-FKBP12 …
- GSM9000647 RNA-seq in ADNP-FKBP12 CTCF-FKBP12 mESC, ctrl, 24h, replicate 3 RNA-seq in ADNP-FKBP12 …
- GSM9000648 RNA-seq in ADNP-FKBP12 CTCF-FKBP12 mESC, dTAG13, 24h, replicate 1 RNA-seq in ADNP-FKBP12 …
- GSM9000649 RNA-seq in ADNP-FKBP12 CTCF-FKBP12 mESC, dTAG13, 24h, replicate 2 RNA-seq in ADNP-FKBP12 …
- GSM9000650 RNA-seq in ADNP-FKBP12 CTCF-FKBP12 mESC, dTAG13, 24h, replicate 3 RNA-seq in ADNP-FKBP12 …
- GSM9000651 RNA-seq in CTCF-FKBP12 mESC, ctrl, 24h, replicate 1 RNA-seq in CTCF-FKBP12 …
- GSM9000652 RNA-seq in CTCF-FKBP12 mESC, ctrl, 24h, replicate 2 RNA-seq in CTCF-FKBP12 …
- GSM9000653 RNA-seq in CTCF-FKBP12 mESC, ctrl, 24h, replicate 3 RNA-seq in CTCF-FKBP12 …
- GSM9000654 RNA-seq in CTCF-FKBP12 mESC, dTAG13, 24h, replicate 1 RNA-seq in CTCF-FKBP12 …
- GSM9000655 RNA-seq in CTCF-FKBP12 mESC, dTAG13, 24h, replicate 2 RNA-seq in CTCF-FKBP12 …
- GSM9000656 RNA-seq in CTCF-FKBP12 mESC, dTAG13, 24h, replicate 3 RNA-seq in CTCF-FKBP12 …
- GSM9000657 RNA-seq in GTF3C1-FKBP12 mESC, ctrl, 24h, replicate 1 RNA-seq in GTF3C1-FKBP1…
- GSM9000658 RNA-seq in GTF3C1-FKBP12 mESC, ctrl, 24h, replicate 2 RNA-seq in GTF3C1-FKBP1…
- GSM9000659 RNA-seq in GTF3C1-FKBP12 mESC, ctrl, 24h, replicate 3 RNA-seq in GTF3C1-FKBP1…
- GSM9000660 RNA-seq in GTF3C1-FKBP12 mESC, dTAG13, 24h, replicate 1 RNA-seq in GTF3C1-FKBP1…
- GSM9000661 RNA-seq in GTF3C1-FKBP12 mESC, dTAG13, 24h, replicate 2 RNA-seq in GTF3C1-FKBP1…
- GSM9000662 RNA-seq in GTF3C1-FKBP12 mESC, dTAG13, 24h, replicate 3 RNA-seq in GTF3C1-FKBP1…
- GSM9000663 RNA-seq in GTF3C1-FKBP12 mESC, ctrl, 4h, replicate 1 RNA-seq in GTF3C1-FKBP1…
- GSM9000664 RNA-seq in GTF3C1-FKBP12 mESC, ctrl, 4h, replicate 2 RNA-seq in GTF3C1-FKBP1…
- GSM9000665 RNA-seq in GTF3C1-FKBP12 mESC, ctrl, 4h, replicate 3 RNA-seq in GTF3C1-FKBP1…
- GSM9000666 RNA-seq in GTF3C1-FKBP12 mESC, dTAG13, 4h, replicate 1 RNA-seq in GTF3C1-FKBP1…
+ 14 more — browse all 54 samples with per-sample file links →
Datasets on a similar topic
- GSE297837 ChAHP Silences SINE Retrotransposons by Inhibiting TFIIIB Recruitment. 126 samples shares tfiiib, sine, retrotransposons, recruitment, inhibiting, silences, chahp
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- GSE286398 Lysine-specific demethylase 1 regulates hematopoietic stem cell expansion and myeloid cell differentiation [scRNA-seq] 13 samples shares sine, rna-seq
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- GSE293811 Heterozygous Kmt2d loss diminishes enhancers to render medulloblastoma cells vulnerable to combinatory inhibition of lysine demethylation and oxidative phosphorylation [RNA-seq] 10 samples shares sine, rna-seq
- GSE247620 Histone methyltransferase SETDB1 silenced SINE B2 retrotransposons and maintained mitotic cell cycle of neural progenitor cells 22 samples shares sine, retrotransposons
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