GEO series

RNA Sequencing Analysis of Wild Type and ColcreER; Tbx4flox/flox Whole Lung and Mesenchymal Extracellular Vesicle Transcriptomes

GSE129355 Mus musculus (mouse) RNA-seq (gene expression) 12 samples Submitted 2025/03/31 Platform GPL21493

At a glance

RNA-seq (gene expression) · mouse · 12 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: Mus musculus (mouse)
Samples: 12 samples: 4 × WT whole lung vs 4 × WT EV vs 2 × ColcreER; Tbx4flox/flox whole lung vs 2 × ColcreER; Tbx4flox/flox EVGroups 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)

Purpose: The goals of this study are to compare wild type (WT) and ColcreER; Tbx4flox/flox whole lung to lung mesenchymal extracellular vesicle (EV) trasncriptome profilling by RNA sequencing (RNA-seq) and to analyze the differentiated genes. Methods: Total RNA was isolated from WT and ColcreER; Tbx4flox/flox whole lung and cultured lung mesenchymal extracellular vesicle.

Read the full summary ↓

mRNA profiles were generated by deep sequencing, using Illumina HiSeq 3000. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks. Results: Using an optimized data analysis workflow, we mapped about 30 million sequence reads per sample to the mouse genome (build mm9) and identified 16,014 transcripts in the retinas of WT and Nrl−/− mice with BWA workflow and 34,115 transcripts with TopHat workflow. RNA-seq data confirmed stable expression of 25 known housekeeping genes, and 12 of these were validated with qRT–PCR. RNA-seq data had a linear relationship with qRT–PCR for more than four orders of magnitude and a goodness of fit (R2) of 0.8798. Approximately 10% of the transcripts showed differential expression between the WT and Nrl−/− retina, with a fold change ≥1.5 and p value <0.05. Altered expression of 25 genes was confirmed with qRT–PCR, demonstrating the high degree of sensitivity of the RNA-seq method. Hierarchical clustering of differentially expressed genes uncovered several as yet uncharacterized genes that may contribute to retinal function. Data analysis with BWA and TopHat workflows revealed a significant overlap yet provided complementary insights in transcriptome profiling. Conclusions: Our study analyzed transcriptomes of WT and ColcreER; Tbx4flox/flox whole lungs and cultured lung mesenchymal extracellular vesicle, with biologic replicates, generated by RNA-seq technology. This study provides a framework for the application of transcriptome profiling towards characterization of differentiated genes in whole lung and mesenchymal extracellular vesicle of WT and Tbx4creER; Ghrflox/flox mice .

This dataset

Open GSE129355 in finder → Find more mouse 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 GSE129355_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 PRJNA531189 and SRA study SRP191138. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Study design

4 × WT whole lung vs 4 × WT EV vs 2 × ColcreER; Tbx4flox/flox whole lung vs 2 × ColcreER; Tbx4flox/flox EV

Supports a between-group comparison across 12 samples.

How we read this: 4 replicated groups read from 12 sample titles; they account for 12 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

GSM3711545 ColcreER; Tbx4flox/flox whole lung rep1 ColcreER; Tbx4flox/flox…
GSM3711546 ColcreER; Tbx4flox/flox whole lung rep2 ColcreER; Tbx4flox/flox…
GSM3711547 WT whole lung rep1 WT whole lung
GSM3711548 WT whole lung rep2 WT whole lung
GSM3711549 WT whole lung rep3 WT whole lung
GSM3711550 WT whole lung rep4 WT whole lung
GSM3711551 ColcreER; Tbx4flox/flox EV rep1 ColcreER; Tbx4flox/flox…
GSM3711552 ColcreER; Tbx4flox/flox EV rep2 ColcreER; Tbx4flox/flox…
GSM3711553 WT EV rep1 WT EV
GSM3711554 WT EV rep2 WT EV
GSM3711555 WT EV rep3 WT EV
GSM3711556 WT EV rep4 WT EV

Datasets on a similar topic

GSE272476 Neutrophils exposed to a cholesterol metabolite secrete extracellular vesicles that promote epithelial-mesenchymal transition and stemness in breast cancer cells [RNA-seq] 30 samples shares extracellular, mesenchymal, vesicle
GSE297762 Mesenchymal Stem Cell Extracellular Vesicles Ameliorate Radiation-caused Dry Mouth 15 samples shares extracellular, mesenchymal, vesicle
GSE330865 Multiorgan transcriptomics and circulating extracellular vesicle profiling reveal age-dependent systemic vulnerability to isoflurane anesthesia and surgery 120 samples shares extracellular, vesicle
GSE242731 Class switch recombination regulation by extracellular vesicles mediated intercellular epigenomic signaling 48 samples shares extracellular, vesicle
GSE253461 Single-cell transcriptional profiling of wildtype Rosa26(YFP) (Y) and Kras(G12D) p53(-/-) Rosa26-YFP (KPY) lung AT2 epithelial cells, AT2 organoids, and co-cultured mesenchymal cells with temporal resolution 39 samples shares mesenchymal, wild
GSE240538 A bone regenerative strategy based on extracellular vesicles transporting citrate for promoting biomineralization 37 samples shares extracellular, vesicle
GSE292919 Whole transcriptomes analyses of organoids derived from Mist1Cre/ERT2 mice corpus with oxidative stress 27 samples shares transcriptomes, whole
GSE235618 Effect of a dendritic cells derived extracellular vesicle as therapeutic vaccine platform to induce neuroprotective immunity for spinal cord injury 21 samples shares extracellular, vesicle

Search all mouse RNA-seq datasets in GEO →

Share this dataset

Metadata from NCBI GEO, cached and refreshed periodically — the NCBI page above is authoritative. Downloads link straight to NCBI/ENA; nothing is proxied through BioTransfer.