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CTCF regulates wild-type and recombinant AAV gene expression by shaping viral chromatin [CUT&Run]

GSE334008 Homo sapiens (human) ChIP-seq / ATAC-seq (genome binding and open chromatin) 47 samples Submitted 2026/07/27 Platform GPL30173
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 47 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
Homo sapiens (human)
Samples
47 samples: 19 conditions, mostly in duplicateGroups 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 regulates wild-type and recombinant AAV gene expression by shaping viral chromatinbioRxiv : the preprint server for biology · 2026
Summary (written by the submitters)
Recombinant Adeno-Associated Viruses (rAAV) gene therapy vectors have been engineered from wild-type AAV (wtAAV2) by inserting the viral telomeres (that serve as replication and packaging signals) on either side of therapeutic transgenes. However, efficient expression of rAAV transgenes require large doses, leading to sporadic toxic side effects.
Read the full summary ↓
We have identified a novel cis-acting element in wtAAV2 bound by the cellular architectural protein CTCF (CCCTC-binding Factor). This CTCF binding element is necessary for efficient wtAAV2 gene expression and is sufficient to enhance the efficiency of rAAV vector’s ability to express reporter transgenes. Chromatin profiling studies reveal that this CTCF binding element regulates the chromatin landscape of the virus and viral vectors. Our discovery of adding merely 19bp of AAV’s CTCF binding element has generated a promising new rAAV gene therapy platform with enhanced transgene expression without impacting vector packaging capacity.
Published in
CTCF regulates wild-type and recombinant AAV gene expression by shaping viral chromatin
Larsen CIS, Abrahams RR, Guertler R et al. · bioRxiv : the preprint server for biology 2026 · PMID 42282747 · doi:10.64898/2026.06.03.729793
This dataset
Open GSE334008 in finder → Find more human ChIP / ATAC / CUT&Tag 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 GSE334008_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: Look for peak files (.bed, .narrowPeak) and signal tracks (.bigWig) among the supplementary files; the raw reads are on ENA.

Also filed as BioProject PRJNA1473376 and SRA study SRP705903. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 42282747) ↗
Study design
19 conditions, mostly in duplicate
AAV2, igg_ctrl, biol ×4 AAV2CBE, H3K27ac, biol ×3 AAV2CBE, H3K4me3, biol ×3 rAAV2, igg_ctrl, biol ×3 rAAV2CBE, H3K4me3, biol ×3 rAAV2CBE, H3K9me3, biol ×3 rAAV2CBE, igg_ctrl, biol ×3 AAV2, CTCF, biol ×2 +12 more

Supports a between-group comparison across 46 samples.

How we read this: 19 replicated groups read from 47 sample titles; they account for 46 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

+ 7 more — browse all 47 samples with per-sample file links →

Datasets on a similar topic

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