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Respiratory Syncytial virus (RSV) directly binds host microRNAs to de-regulate host gene targets [RNA-seq miR-27 over-expression]

GSE231787 Homo sapiens (human) RNA-seq (gene expression) 19 samples Submitted 2024/05/29 Platform GPL30173
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
RNA-RNA interactions between respiratory syncytial virus and miR-26 and miR-27 are associated with regulation of cell cycle and antiviral immunityNucleic acids research · 2024
Summary (written by the submitters)
To validate miR-27 mRNA targets, we generated miR-27 overexpressing cell lines using the shMIMIC lentiviral transduction system (Dharmacon) In addition, we transfected miR-27 miRNA mimics and inhibitors to overexpress and inhibit the miRNA and performed total RNAseq
Published in
RNA-RNA interactions between respiratory syncytial virus and miR-26 and miR-27 are associated with regulation of cell cycle and antiviral immunity
Ressel S, Kumar S, Bermúdez-Barrientos JR et al. · Nucleic acids research 2024 · PMID 38412296 · doi:10.1093/nar/gkae116
This dataset
Open GSE231787 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 GSE231787_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 PRJNA967684 and SRA study SRP436131. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 38412296) ↗
Study design
7 conditions, mostly in triplicate
A549 miR-27a shMIMIC clone 1, Mock-infected, ×3 A549 WT, Mock-infected ×3 A549 miR-27a & miR-27b mimic transfected, Moc… ×3 A549 miR-27a & miR-27b inhibitor transfected,… ×3 A549 NTC shMIMIC clone 1, Mock-infected ×2 A549 control mimic transfected, Mock-infected, ×2 A549 control inhibitor transfected, Mock-infe… ×2 A549 non-targeting control (NTC) shMIMIC clon… ×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
Datasets on a similar topic

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