GEO series

The RNA binding protein Bcas2 is necessary for antibody class switch in mammalian genomes

GSE271398 Homo sapiens (human) RNA-seq (gene expression) 14 samples Submitted 2025/07/02 Platform GPL17021Platform GPL16791

At a glance

RNA-seq (gene expression) · human · 14 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: 14 samples: 7 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: The RNA Binding Protein Bcas2 is Required for Antibody Class Switch in Activated-B CellsExploration (Beijing, China) · 2025

Summary (written by the submitters)

In children, hyper-IgM syndrome type 1 (HIGM1) is a type of severe antibody disorder, the pathogenesis of which remains unclear. Here we report for the first time that breast cancer amplified sequence 2 (BCAS2), known as an RNA-binding protein, regulates the antibody class transition processes through alternative splicing (AS). Based on integrated analysis of the whole genome sequence and CLIP-seq data, we revealed that BCAS2 regulates AS through binding to the GAAGAA motif of target genes in B cells.

Read the full summary ↓

Besides, BCAS2 can interact with SRSF7/DHX15 proteins and form spliceosomes that regulates AS and mRNA levels of target genes. In HIGM2 patients, BCAS2 affected the AS and expression of key target genes, and consequently the serum antibody levels. Collectively, the results in this study show that Bcas2 forms a complex with factors such as SRSF7 to regulate AS of key genes, thereby affecting the antibody production. The deletion or reduced expression of BCAS2 may lead to the HIGM2 phenotype. The present study reveals for the first time the pathogenesis of HIGM2, providing a potential molecular target for treatment of the disease.

Published in

The RNA Binding Protein Bcas2 is Required for Antibody Class Switch in Activated-B Cells

Chen Y, Sun S, Lu C et al. · Exploration (Beijing, China) 2025 · PMID 40585763 · doi:10.1002/EXP.70015

This dataset

Open GSE271398 in finder → Find more 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 GSE271398_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 PRJNA1131328 and SRA study SRP517758. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40585763) ↗

Study design

7 conditions, mostly in duplicate

CLIP-seq_BCAS_SpB ×2 CLIP-seq_BCAS_SpB_LPS ×2 CLIP-seq_BCAS_SpB_IgG ×2 RNA-seq_cKO ×2 RNA-seq_CTRL ×2 RNA-seq_Healthy_person ×2 RNA-seq_HIGM1_patient ×2

Supports a case/control comparison: 2 samples read as cases, 4 as controls.

How we read this: 7 replicated groups read from 14 sample titles; they account for 14 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

GSM8376175 CLIP-seq_BCAS_SpB_rep1 CLIP-seq_BCAS_SpB
GSM8376176 CLIP-seq_BCAS_SpB_rep2 CLIP-seq_BCAS_SpB
GSM8376177 CLIP-seq_BCAS_SpB_LPS_rep1 CLIP-seq_BCAS_SpB_LPS
GSM8376178 CLIP-seq_BCAS_SpB_LPS_rep2 CLIP-seq_BCAS_SpB_LPS
GSM8376179 CLIP-seq_BCAS_SpB_IgG_rep1 CLIP-seq_BCAS_SpB_IgG
GSM8376180 CLIP-seq_BCAS_SpB_IgG_rep2 CLIP-seq_BCAS_SpB_IgG
GSM8376181 RNA-seq_cKO_rep1 RNA-seq_cKO
GSM8376182 RNA-seq_cKO_rep2 RNA-seq_cKO
GSM8376183 RNA-seq_CTRL_rep1 RNA-seq_CTRL
GSM8376184 RNA-seq_CTRL_rep2 RNA-seq_CTRL
GSM8691749 RNA-seq_Healthy_person_1 RNA-seq_Healthy_person
GSM8691750 RNA-seq_Healthy_person_2 RNA-seq_Healthy_person
GSM8691751 RNA-seq_HIGM1_patient_1 RNA-seq_HIGM1_patient
GSM8691752 RNA-seq_HIGM1_patient_2 RNA-seq_HIGM1_patient

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