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LncRNAs regulate FBL to facilitate rRNA processing in cancer cells

GSE276144 Homo sapiens (human) ChIP-seq / ATAC-seq (genome binding and open chromatin) 11 samples Submitted 2025/03/26 Platform GPL24676
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 11 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
11 samples: 5 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
lncRNAs maintain the functional phase state of nucleolar prion-like protein to facilitate rRNA processingMolecular cell · 2024
Summary (written by the submitters)
We identified lncRNA DNAJC3-AS1 can buffer the behavior of FBL condensation in cancer cell. In this study, we preformed the FBL-TurboID-RIP and Single-end Enhanced Cross-linking and Immunoprecipitation (seCLIP) sequencing to to identify candidate RNAs that bind to FBL or its adjacent proteins. The FBL-binding regions distributed throughout the sequence of lncRNAs were also discovered.
Published in
lncRNAs maintain the functional phase state of nucleolar prion-like protein to facilitate rRNA processing
Sun YM, Zhu SX, Chen XT et al. · Molecular cell 2024 · PMID 39579766 · doi:10.1016/j.molcel.2024.10.036
This dataset
Open GSE276144 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 GSE276144_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 PRJNA1155179 and SRA study SRP529915. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39579766) ↗
Study design
5 conditions, mostly in duplicate
FBL_clip seq ×3 molm13_TurboID-RIP seq_NC ×2 molm13_FBL-TurboID-RIP seq ×2 sw480_TurboID-RIP seq_NC ×2 sw480_FBL-TurboID-RIP seq ×2

Supports a between-group comparison across 11 samples.

How we read this: 5 replicated groups read from 11 sample titles; they account for 11 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
Datasets on a similar topic

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