GEO series
BAHCC1 promotes gene expression in neuronal cells by antagonizing SIN3A-HDAC1
GSE281267
Mus musculus (mouse)
ChIP-seq / ATAC-seq (genome binding and open chromatin)
149 samples
Submitted 2025/06/12
Platform GPL34328Platform GPL24247
At a glance
ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 149 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
- 149 samples: 45 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
- BAHCC1 promotes gene expression in neuronal cells by antagonizing SIN3A-HDAC1Nucleic acids research · 2025
Summary (written by the submitters)
Chromatin modifications play a key role in the regulation of gene expression during development and adult physiology. Histone acetylation, and in particular H3K27ac is associated with increased activity of gene regulatory elements. The regulation of the machinery that deposits or strips this modification remains poorly understood. In particular, the SIN3A-HDAC1 complex possesses a histone deacetylation activity, yet it commonly resides at active regulatory regions.
Read the full summary ↓
Here, we study BAHCC1, a large chromatin-associated protein essential for viability, and recently reported to play a largely repressive role. We show that in cells of the neuronal lineage, BAHCC1 is most associated with regulatory elements marked with H3K27ac. BAHCC1 interacts and co-occupies shared genomic regions with the SIN3A scaffold protein and its perturbations lead to decreased acetylation and decreased expression of the proximal genes in a neuronal cell line and in primary cortical neurons. The regulated genes are enriched for those functioning in neurogenesis and cell migration. We propose a model in which BAHCC1 antagonizes SIN3A histone deacetylation and positively regulates the expression of genes important in the neuronal lineage.
Published in
Monziani A, Perry RB, Hezroni H et al.
· Nucleic acids research 2025
· PMID 40682820
· doi:10.1093/nar/gkaf650
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 GSE281267_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 PRJNA1182856 and SRA study SRP543695. Searching any of these in the dataset finder brings you back here.
Study design
45 conditions, mostly in triplicate
CUT&RUN for BAHCC1 in N2a cells, ×4
RNA-seq in N2a cells after transfection with … ×3
RNA-seq in N2a cells after transfection with … ×3
RNA-seq in N2a cells after transfection with … ×3
RNA-seq in N2a cells after transfection with … ×3
RNA-seq in differentiated N2a cells after tra… ×3
RNA-seq in differentiated N2a cells after tra… ×3
RNA-seq in N2a cells after transfection with … ×3
+58 more
Supports a between-group comparison across 128 samples.
How we read this: 45 replicated groups read from 149 sample titles; they account for 128 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
- GSM8616505 RNA-seq in N2a cells after transfection with siRNAs against Bahcc1, replicate 1 RNA-seq in N2a cells af…
- GSM8616506 RNA-seq in N2a cells after transfection with siRNAs against Bahcc1, replicate 2 RNA-seq in N2a cells af…
- GSM8616507 RNA-seq in N2a cells after transfection with siRNAs against Bahcc1, replicate 3 RNA-seq in N2a cells af…
- GSM8616508 RNA-seq in N2a cells after transfection with control siRNAs, replicate 1 (siBahcc1 experiment)
- GSM8616509 RNA-seq in N2a cells after transfection with control siRNAs, replicate 2 (siBahcc1 experiment)
- GSM8616510 RNA-seq in N2a cells after transfection with control siRNAs, replicate 3 (siBahcc1 experiment)
- GSM8616511 RNA-seq in N2a cells after transfection with GapmeRs targeting Bahcc1, replicate 1 RNA-seq in N2a cells af…
- GSM8616512 RNA-seq in N2a cells after transfection with GapmeRs targeting Bahcc1, replicate 2 RNA-seq in N2a cells af…
- GSM8616513 RNA-seq in N2a cells after transfection with GapmeRs targeting Bahcc1, replicate 3 RNA-seq in N2a cells af…
- GSM8616514 RNA-seq in N2a cells after transfection with control GapmeRs, replicate 1 RNA-seq in N2a cells af…
- GSM8616515 RNA-seq in N2a cells after transfection with control GapmeRs, replicate 2 RNA-seq in N2a cells af…
- GSM8616516 RNA-seq in N2a cells after transfection with control GapmeRs, replicate 3 RNA-seq in N2a cells af…
- GSM8616517 RNA-seq in N2a cells after transfection with control GapmeRs and DMSO, replicate 1 RNA-seq in N2a cells af…
- GSM8616518 RNA-seq in N2a cells after transfection with control GapmeRs and DMSO, replicate 2 RNA-seq in N2a cells af…
- GSM8616519 RNA-seq in N2a cells after transfection with control GapmeRs and DMSO, replicate 3 RNA-seq in N2a cells af…
- GSM8616520 RNA-seq in differentiated N2a cells after transfection with control GapmeRs, replicate 1 RNA-seq in differentiat…
- GSM8616521 RNA-seq in differentiated N2a cells after transfection with control GapmeRs, replicate 2 RNA-seq in differentiat…
- GSM8616522 RNA-seq in differentiated N2a cells after transfection with control GapmeRs, replicate 3 RNA-seq in differentiat…
- GSM8616523 RNA-seq in differentiated N2a cells after transfection with GapmeRs targeting Bahcc1, replicate 1 RNA-seq in differentiat…
- GSM8616524 RNA-seq in differentiated N2a cells after transfection with GapmeRs targeting Bahcc1, replicate 2 RNA-seq in differentiat…
- GSM8616525 RNA-seq in differentiated N2a cells after transfection with GapmeRs targeting Bahcc1, replicate 3 RNA-seq in differentiat…
- GSM8616526 RNA-seq in N2a cells after transfection with the EV, replicate 1 (Bahcc1 OE control)
- GSM8616527 RNA-seq in N2a cells after transfection with the EV, replicate 2 (Bahcc1 OE control)
- GSM8616528 RNA-seq in N2a cells after transfection with the EV, replicate 3 (Bahcc1 OE control)
- GSM8616529 RNA-seq in N2a cells after transfection with the Bahcc1 OE vector, replicate 1 RNA-seq in N2a cells af…
- GSM8616530 RNA-seq in N2a cells after transfection with the Bahcc1 OE vector, replicate 2 RNA-seq in N2a cells af…
- GSM8616531 RNA-seq in N2a cells after transfection with the Bahcc1 OE vector, replicate 3 RNA-seq in N2a cells af…
- GSM8616532 RNA-seq in N2a cells after transfection with the EV, replicate 1 (Reno1 OE control)
- GSM8616533 RNA-seq in N2a cells after transfection with the EV, replicate 2 (Reno1 OE control)
- GSM8616534 RNA-seq in N2a cells after transfection with the EV, replicate 3 (Reno1 OE control)
- GSM8616535 RNA-seq in N2a cells after transfection with the Reno1 OE vector, replicate 1 RNA-seq in N2a cells af…
- GSM8616536 RNA-seq in N2a cells after transfection with the Reno1 OE vector, replicate 2 RNA-seq in N2a cells af…
- GSM8616537 RNA-seq in N2a cells after transfection with the Reno1 OE vector, replicate 3 RNA-seq in N2a cells af…
- GSM8616538 RNA-seq in N2a cells after transfection with siRNAs against Sin3a, replicate 1 RNA-seq in N2a cells af…
- GSM8616539 RNA-seq in N2a cells after transfection with siRNAs against Sin3a, replicate 2 RNA-seq in N2a cells af…
- GSM8616540 RNA-seq in N2a cells after transfection with siRNAs against Sin3a, replicate 3 RNA-seq in N2a cells af…
- GSM8616541 RNA-seq in N2a cells after transfection with siRNAs against Fam60a, replicate 1 RNA-seq in N2a cells af…
- GSM8616542 RNA-seq in N2a cells after transfection with siRNAs against Fam60a, replicate 2 RNA-seq in N2a cells af…
- GSM8616543 RNA-seq in N2a cells after transfection with siRNAs against Fam60a, replicate 3 RNA-seq in N2a cells af…
- GSM8616544 RNA-seq in N2a cells after transfection with control siRNAs, replicate 1 (siSin3a/siFam60a experiment)
+ 109 more — browse all 149 samples with per-sample file links →
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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.