GEO series

Paraspeckle-Independent Co-Transcriptional Regulation of Nuclear microRNA Biogenesis by SFPQ [RNA-seq]

GSE262125 Homo sapiens (human) RNA-seq (gene expression) 24 samples Submitted 2024/09/04 Platform GPL18573

At a glance

RNA-seq (gene expression) · human · 24 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: 24 samples: 8 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: Paraspeckle-independent co-transcriptional regulation of nuclear microRNA biogenesis by SFPQCell reports · 2024

Summary (written by the submitters)

MicroRNAs (miRNAs) play crucial roles in physiological functions and diseases such as cancer, but the regulation of their nuclear biogenesis remains poorly understood. Here, BioID on Drosha, the catalytic subunit of the microprocessor complex, revealed its proximity to SFPQ, a multifunctional RNA-binding protein (RBP) notably involved in forming the paraspeckle nuclear condensates.

Read the full summary ↓

SFPQ depletion impacted both primary and mature miRNA expression, while other crucial paraspeckle proteins or the paraspeckle scaffolding lncRNA NEAT1 did not, indicating a unique paraspeckle-independent role. Comprehensive transcriptomic analyses showed that SFPQ loss broadly affects RNA and miRNA host gene (miRNA HG) expression, influencing both their transcription and stability. Notably, SFPQ protects specific miRNA HGs, including the oncogenic miR-17~92 polycistron, from degradation by the nuclear NEXT-exosome complex. Lastly, we show that high SFPQ is tightly linked with overexpression miR-17~92 and its mature miRNAs across a broad variety of cancers. Our findings reveal a dual role for SFPQ in the regulation of miRNA HGs transcription and stability, as well as its significance in cancers.

Published in

Paraspeckle-independent co-transcriptional regulation of nuclear microRNA biogenesis by SFPQ

Thivierge C, Bellefeuille M, Diwan SS et al. · Cell reports 2024 · PMID 39250314 · doi:10.1016/j.celrep.2024.114695

This dataset

Open GSE262125 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 GSE262125_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 PRJNA1090439 and SRA study SRP496963. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39250314) ↗

Study design

8 conditions, mostly in triplicate

SBC-3, siCtrl, RNA-seq ×3 SBC-3, siSFPQ-2, RNA-seq ×3 SBC-3, siSFPQ-3, RNA-seq ×3 SBC-3, siNONO-3, RNA-seq ×3 SBC-3, siNONO-4, RNA-seq ×3 SBC-3, ASO-Ctrl, RNA-seq ×3 SBC-3, ASO-NEAT1-1047, RNA-seq ×3 SBC-3, ASO-NEAT1-1473, RNA-seq ×3

Supports a between-group comparison across 24 samples.

How we read this: 8 replicated groups read from 24 sample titles; they account for 24 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

GSM8157940 SBC-3, siCtrl, RNA-seq rep.1 SBC-3, siCtrl, RNA-seq
GSM8157941 SBC-3, siCtrl, RNA-seq rep.2 SBC-3, siCtrl, RNA-seq
GSM8157942 SBC-3, siCtrl, RNA-seq rep.3 SBC-3, siCtrl, RNA-seq
GSM8157943 SBC-3, siSFPQ-2, RNA-seq rep.1 SBC-3, siSFPQ-2, RNA-seq
GSM8157944 SBC-3, siSFPQ-2, RNA-seq rep.2 SBC-3, siSFPQ-2, RNA-seq
GSM8157945 SBC-3, siSFPQ-2, RNA-seq rep.3 SBC-3, siSFPQ-2, RNA-seq
GSM8157946 SBC-3, siSFPQ-3, RNA-seq rep.1 SBC-3, siSFPQ-3, RNA-seq
GSM8157947 SBC-3, siSFPQ-3, RNA-seq rep.2 SBC-3, siSFPQ-3, RNA-seq
GSM8157948 SBC-3, siSFPQ-3, RNA-seq rep.3 SBC-3, siSFPQ-3, RNA-seq
GSM8157949 SBC-3, siNONO-3, RNA-seq rep.1 SBC-3, siNONO-3, RNA-seq
GSM8157950 SBC-3, siNONO-3, RNA-seq rep.2 SBC-3, siNONO-3, RNA-seq
GSM8157951 SBC-3, siNONO-3, RNA-seq rep.3 SBC-3, siNONO-3, RNA-seq
GSM8157952 SBC-3, siNONO-4, RNA-seq rep.1 SBC-3, siNONO-4, RNA-seq
GSM8157953 SBC-3, siNONO-4, RNA-seq rep.2 SBC-3, siNONO-4, RNA-seq
GSM8157954 SBC-3, siNONO-4, RNA-seq rep.3 SBC-3, siNONO-4, RNA-seq
GSM8157955 SBC-3, ASO-Ctrl, RNA-seq rep.1 SBC-3, ASO-Ctrl, RNA-seq
GSM8157956 SBC-3, ASO-Ctrl, RNA-seq rep.2 SBC-3, ASO-Ctrl, RNA-seq
GSM8157957 SBC-3, ASO-Ctrl, RNA-seq rep.3 SBC-3, ASO-Ctrl, RNA-seq
GSM8157958 SBC-3, ASO-NEAT1-1047, RNA-seq rep.1 SBC-3, ASO-NEAT1-1047, …
GSM8157959 SBC-3, ASO-NEAT1-1047, RNA-seq rep.2 SBC-3, ASO-NEAT1-1047, …
GSM8157960 SBC-3, ASO-NEAT1-1047, RNA-seq rep.3 SBC-3, ASO-NEAT1-1047, …
GSM8157961 SBC-3, ASO-NEAT1-1473, RNA-seq rep.1 SBC-3, ASO-NEAT1-1473, …
GSM8157962 SBC-3, ASO-NEAT1-1473, RNA-seq rep.2 SBC-3, ASO-NEAT1-1473, …
GSM8157963 SBC-3, ASO-NEAT1-1473, RNA-seq rep.3 SBC-3, ASO-NEAT1-1473, …

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