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RNA and PTBP1-RIP sequencing in BEAS-2B cells with circFCHO2 overexpression and knockdown

GSE286017 Homo sapiens (human) RNA-seq (gene expression) 16 samples Submitted 2025/08/09 Platform GPL24676
At a glance

RNA-seq (gene expression) · human · 16 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
Homo sapiens (human)
Samples
16 samples: 2 × Control_OE_RNA vs 2 × Control_KD_RNA vs 2 × circFCHO2_OE_RNA vs 2 × circFCHO2_KD_RNAGroups 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
Circular RNA FCHO2 promotes airway remodeling in COPD via regulating nuclear translocation of PTBP1 to repress the splicing of GRN pre-mRNACell death & disease · 2025
Summary (written by the submitters)
Circular RNAs (circRNAs) have emerged as key regulators in human diseases, yet their mechanisms of action in chronic obstructive pulmonary disease (COPD) remain largely unknown. We report a mammalian conserved circRNA circFCHO2 is identified to play critical roles in COPD. The expression level of circFCHO2 was significantly increased in COPD cell models, mouse models, and human lung tissue samples.
Read the full summary ↓
Meanwhile, we demonstrated that circFCHO2 promotes epithelial-to-mesenchymal transition (EMT) of bronchial epithelial cells and extracellular matrix (ECM) remodeling. Mechanistically, circFCHO2 binds to and facilitates the nuclear translocation of PTBP1, thereby inhibiting the splicing of GRN pre-mRNA, which reduces PGRN protein expression levels. This activation of the NF-κB signaling pathway regulates the expression of EMT and ECM remodeling-related proteins, leading to the occurrence of airway remodeling. Overall, our study advanced the understanding of the molecular mechanisms by which circRNAs contribute to the airway remodeling of COPD.
Published in
Circular RNA FCHO2 promotes airway remodeling in COPD via regulating nuclear translocation of PTBP1 to repress the splicing of GRN pre-mRNA
Liu Y, Wang Y, Fei Y et al. · Cell death & disease 2025 · PMID 41184265 · doi:10.1038/s41419-025-08107-9
This dataset
Open GSE286017 in finder → Find more human RNA-seq 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 GSE286017_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: 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 PRJNA1207501 and SRA study SRP555801. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41184265) ↗
Study design
2 × Control_OE_RNA vs 2 × Control_KD_RNA vs 2 × circFCHO2_OE_RNA vs 2 × circFCHO2_KD_RNA

Supports a between-group comparison across 8 samples.

How we read this: 4 replicated groups read from 16 sample titles; they account for 8 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
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