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BCOR mutations deregulate cell cycle and hypoxic adaptation pathways in retinoblastoma

GSE314545 Homo sapiens (human) RNA-seq (gene expression) 19 samples Submitted 2026/03/23 Platform GPL24676
At a glance

RNA-seq (gene expression) · human · 19 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
19 samples: 7 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
BCOR Mutations Deregulate Cell Cycle and Hypoxic Adaptation Pathways in RetinoblastomaMolecular cancer research : MCR · 2026
Summary (written by the submitters)
Retinoblastoma (RB) is the most common pediatric eye cancer. Most cases of RB are initiated by bi-allelic mutational inactivation of the RB1 gene. After RB1, the gene that is most commonly mutated gene in RB is BCOR, which is mutated in approximately 20% of RB tumors and is associated with a more aggressive tumor phenotype and worse patient outcomes. Here, we interrogated BCOR in low passage RB cell lines using RNA sequencing. We show that loss of BCOR downregulates the expression of genes associated with cell cycle regulation and upregulates genes associated with hypoxic adaptation.
Published in
BCOR Mutations Deregulate Cell Cycle and Hypoxic Adaptation Pathways in Retinoblastoma
Zhang MG, Kuznetsoff JN, Cetta NC et al. · Molecular cancer research : MCR 2026 · PMID 41191430 · doi:10.1158/1541-7786.MCR-24-1078
This dataset
Open GSE314545 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 GSE314545_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 PRJNA1391482 and SRA study SRP656795. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41191430) ↗
Study design
7 conditions, mostly in triplicate
Low passage retinoblastoma cell line RB006, e… ×3 Low passage retinoblastoma cell line RB006 wi… ×3 Low passage retinoblastoma cell line RB028, e… ×3 Low passage retinoblastoma cell line RB028 wi… ×3 Low passage retinoblastoma cell line RB016, ×2 Low passage retinoblastoma cell line RB026, ×2 Low passage retinoblastoma cell line WRB06, ×2 Low passage retinoblastoma cell line RB018, ×1

Supports a between-group comparison across 18 samples.

How we read this: 7 replicated groups read from 19 sample titles; they account for 18 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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