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Systems analysis of miR-199a/b-5p and multiple miR-199a/b-5p targets during chondrogenesis

GSE274379 Homo sapiens (human) RNA-seq (gene expression) 18 samples Submitted 2024/08/09 Platform GPL18573
At a glance

RNA-seq (gene expression) · human · 18 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
18 samples: 6 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
Systems analysis of miR-199a/b-5p and multiple miR-199a/b-5p targets during chondrogenesiseLife · 2024
Summary (written by the submitters)
Changes in chondrocyte gene expression can contribute to the development of osteoarthritis (OA), and so recognition of the regulative processes during chondrogenesis can lead to a better understanding of OA. microRNAs (miRNAs) are key regulators of gene expression in chondrocytes/OA and we have used a combined experimental, bioinformatic, and systems biology approach to explore the multiple miRNA-mRNA interactions that regulate chondrogenesis.
Read the full summary ↓
A longitudinal chondrogenesis bioinformatic analysis identified paralogues miR-199a-5p and miR-199b-5p as pro-chondrogenic regulators. Experimental work demonstrated alteration of miR-199a-5p or miR-199b-5p expression led to significant inverse modulation of key chondrogenic genes and extracellular matrix production. miR-199a/b-5p targetsFZD6, ITGA3andCAV1were identified by inhibition experiments and verified as direct targets by luciferase assay. The experimental work was used to generate and parameterize a multi-miRNA 14-day chondrogenesis kinetic model to be used as a repository for the experimental work and as a resource for further investigation of this system. This is the first multi-miRNA model of a chondrogenesis-based system, and highlights the complex relationships between regulatory miRNAs, and their target mRNAs.
Published in
Systems analysis of miR-199a/b-5p and multiple miR-199a/b-5p targets during chondrogenesis
Patel K, Barter M, Soul J et al. · eLife 2024 · PMID 39401064 · doi:10.7554/eLife.89701
This dataset
Open GSE274379 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 GSE274379_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 PRJNA1146147 and SRA study SRP525204. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39401064) ↗
Study design
6 conditions, mostly in triplicate
MSC, day 0, hairpin control, sample ×3 MSC, day 0, hairpin inhibitor miR-199a-5p, sa… ×3 MSC, day 0, hairpin inhibitor miR-199b-5p, sa… ×3 MSC, day 1, hairpin control, sample ×3 MSC, day 1, hairpin inhibitor miR-199a-5p, sa… ×3 MSC, day 1, hairpin inhibitor miR-199b-5p, sa… ×3

Supports a between-group comparison across 18 samples.

How we read this: 6 replicated groups read from 18 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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