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Deciphering the novel regulatory mechanisms and biological implications of ARID1A C-terminal missense mutations in cancer [RNA-seq]

GSE254867 Homo sapiens (human) RNA-seq (gene expression) 27 samples Submitted 2024/10/09 Platform GPL24676
At a glance

RNA-seq (gene expression) · human · 27 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
27 samples: 9 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.
Summary (written by the submitters)
ARID1A (the AT-rich interaction domain 1A, also known as BAF250a), a pivotal component of the SWI/SNF chromatin remodeling complex, is frequently mutated in various cancers. In this study, we discovered that mutations such as ARID1A V2084D or V2087E lead to the binding of ARID1A mutant with the nucleocytoplasmic shuttling protein XPO1, facilitating ARID1A mutant transport to the cytoplasm.
Read the full summary ↓
Subsequently, the E3 ubiquitin ligase STUB1 recognizes and ubiquitinates ARID1A mutant protein, marking it for degradation. This reduction in protein levels due to the mutation impedes the assembly of the cBAF complex and the expression of tumor-suppressive target genes, ultimately contributing to a malignant phenotype. Knocked down STUB1 or inhibit XPO1 activity stabilizes the ARID1A mutant protein, retaining it in the nucleus, which restores the assembly of the cBAF complex, chromatin remodeling function, and the expression of critical genes, thereby decrease the tumor burden.
This dataset
Open GSE254867 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 GSE254867_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 PRJNA1072107 and SRA study SRP487533. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
9 conditions, mostly in triplicate
293T_KO ×3 293T_KO_ARID1A_WT ×3 293T_KO_ARID1A_V2084D ×3 293T_KO_ARID1A_G2087E ×3 293T_KO_ARID1A_G2087R ×3 293T_KO_ARID1A_K2025E ×3 Huh7_KO_ARID1A_WT ×3 Huh7_KO_ARID1A_V2084D ×3 +1 more

Supports a between-group comparison across 27 samples.

How we read this: 9 replicated groups read from 27 sample titles; they account for 27 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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