GEO series

AKAP95 condensates regulate transcription and can be targeted in MLL-fusion driven oncogenesis (ChIP-Seq)

GSE271854 Homo sapiens (human) ChIP-seq / ATAC-seq (genome binding and open chromatin) 23 samples Submitted 2025/11/11 Platform GPL34281Platform GPL30173

At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 23 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: 23 samples: 21 distinct titles, 2 of them repeatedGroups 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.

Summary (written by the submitters)

Oncogenic transcription represents a crucial event in MLL rearranged (MLLr) leukemia, yet the precise role of transcription co-activators in MLL-fusion protein-associated transcription and their contribution to leukemogenesis remain incompletely understood. Here, we demonstrate that AKAP95 is notably up-regulated in both MLLr patients and in MLL-AF9-transformed mouse bone marrow.

Read the full summary ↓

AKAP95 proves essential for initiating mouse MLL-AF9 leukemia, exhibiting widespread DNA binding across the genome, particularly at gene promoters. Interaction with the translocated MLL1 fragment primarily occurs through phase separation mechanisms. AKAP95's RNA-binding properties, coupled with its phase separation behavior, govern its binding to pre-mRNA and concurrent transcriptional regulation. Importantly, we engineered a peptide to disrupt its phase separation, effectively attenuating AKAP95-mediated transcriptional co-activation and inhibiting the growth of MLLr cell lines. These findings illustrate a vivid example of an RNA-binding protein orchestrating transcription and tumorigenesis via phase separation, underscoring the potential for targeting oncogenic condensation mechanisms therapeutically.

This dataset

Open GSE271854 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 GSE271854_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 PRJNA1133759 and SRA study SRP518850. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Study design

21 distinct titles, 2 of them repeated

WT_H3K4Me ×2 KO_H3K4Me ×2

How we read this: Read from 23 sample titles: 21 distinct titles with little repetition. 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

GSM8387177 DMSO
GSM8387178 High_ActD
GSM8387179 Low_ActD
GSM8387180 WT_INPUT
GSM8387181 KO_INPUT
GSM8387182 WT_H3K4Me1
GSM8387183 KO_H3K4Me1
GSM8387184 WT_H3K4Me3
GSM8387185 KO_H3K4Me3
GSM8387186 WT_H3K27Ac
GSM8387187 KO_H3K27Ac
GSM8387188 AKAP_WT_ChIP
GSM8387189 AKAP_KI_ChIP
GSM8387190 PSmut_PolII_CHIP
GSM8387191 WT_PolII_CHIP
GSM8387192 ZFmut_PolII_CHIP
GSM8387193 PSmut_S2P_CHIP
GSM8387194 WT_S2P_CHIP
GSM8387195 ZFmut_S2P_CHIP
GSM9141749 KD-rescued with vector control-CHIP-Seq
GSM9141750 KD-rescued with PS-mut-CHIP-Seq
GSM9141751 KD-rescued with ZF-mut-CHIP-Seq
GSM9141752 KD-rescued with AKAP-WT-CHIP-Seq

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Search all human ChIP / ATAC / CUT&Tag datasets in GEO →

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