GEO series

Comparing gene expression across primary human airway models for cystic fibrosis precision medicine

GSE172232 Homo sapiens (human) RNA-seq (gene expression) 71 samples Submitted 2021/11/15 Platform GPL16791

At a glance

RNA-seq (gene expression) · human · 71 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: 71 samples
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)

Rationale:Cultured human bronchial epithelia (HBE) are the gold standard model for assessing the efficacy of small molecule therapies in cystic fibrosis (CF). However, these cells are difficult to access, especially in young children. Human nasal epithelia (HNE) are used as a surrogate model although it is unknown whether HNE recapitulate the gene expression properties of HBE Objective: To investigate the similarities and differences in gene expression genome-wide between HBE and HNE with a focus on CF lung disease modifier genes.

Read the full summary ↓

Methods: RNA-sequencing was conducted on paired cultured and naïve HNE and HBE (n=71 samples) collected from 21 patients with CF who underwent lung transplantation. Gene expression was first compared across cultured and naïve samples to assess the impact of the culturing process, then compared between cultured HNE and HBE. Co-expression relationships of CF modifier genes were compared between cultured HNE and HBE. Results: The culturing process had little impact on the expression level of CF lung disease modifier genes. These genes also showed significant equivalent expression between cultured HNE and HBE. Their co-expression relationships in cultured HNE and HBE overlapped significantly, suggesting the corresponding biological processes are consistent across the two tissues. Conclusions: CF lung disease modifier genes have similar expression profiles across cultured HNE and HBE. This supports the use of HNE as a surrogate airway model to investigate CF lung disease, modifier genes and enable investigation of CF precision medicine.

This dataset

Open GSE172232 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 GSE172232_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 PRJNA722498 and SRA study SRP315120. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Samples in this study

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+ 71 more — browse all 71 samples with per-sample file links →

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