GEO series

control versus allergic rhinitis basal cells in response to Der p1

GSE288682 Homo sapiens (human) RNA-seq (gene expression) 36 samples Submitted 2025/04/01 Platform GPL30173

At a glance

RNA-seq (gene expression) · human · 36 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: 36 samples: 6 conditions, mostly with about 6 replicates eachGroups 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)

Basal cells are the epithelial progenitor cells of the airways and play a critical role in tissue homeostasis and repair. In a healthy upper airway epithelium, the basal cells are usually shielded from environmental triggers as they are positioned in close contact with the basement membrane. In allergic rhinitis, it is known that the epithelial barrier is dysfunctional and it is believed that in this situation basal cells become more accessible to airborne particles, however, it is not known whether basal cells can sense these triggers directly.

Read the full summary ↓

In addition, previous research has shown that control basal cells phenotypically and functionally differ from allergic rhinitis (AR) basal cells. In this study, we aimed to further compare phenotypical differences between sorted primary control and house dust mite (HDM)-allergic AR basal cells, before and after culture, using bulk RNA sequencing. Moreover, we wanted to evaluate the basal cell transcriptional response to HDM-derived Der p1 to study their potential as an environmental sensor.

This dataset

Open GSE288682 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 GSE288682_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 PRJNA1219057 and SRA study SRP561434. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Study design

6 conditions, mostly with about 6 replicates each

airway basal cells, control, fresh, ×6 airway basal cells, control, culture, ×6 airway basal cells, control, Der p1, ×6 airway basal cells, AR, fresh, ×6 airway basal cells, AR, culture, ×6 airway basal cells, AR, Der p1, ×6

Supports a between-group comparison across 36 samples.

How we read this: 6 replicated groups read from 36 sample titles; they account for 36 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

GSM8772995 airway basal cells, control, fresh, 1 airway basal cells, con…
GSM8772996 airway basal cells, control, culture, 1 airway basal cells, con…
GSM8772997 airway basal cells, control, Der p1, 1 airway basal cells, con…
GSM8772998 airway basal cells, control, fresh, 2 airway basal cells, con…
GSM8772999 airway basal cells, control, culture, 2 airway basal cells, con…
GSM8773000 airway basal cells, control, Der p1, 2 airway basal cells, con…
GSM8773001 airway basal cells, control, fresh, 3 airway basal cells, con…
GSM8773002 airway basal cells, control, culture, 3 airway basal cells, con…
GSM8773003 airway basal cells, control, Der p1, 3 airway basal cells, con…
GSM8773004 airway basal cells, control, fresh, 4 airway basal cells, con…
GSM8773005 airway basal cells, control, culture, 4 airway basal cells, con…
GSM8773006 airway basal cells, control, Der p1, 4 airway basal cells, con…
GSM8773007 airway basal cells, control, fresh, 5 airway basal cells, con…
GSM8773008 airway basal cells, control, culture, 5 airway basal cells, con…
GSM8773009 airway basal cells, control, Der p1, 5 airway basal cells, con…
GSM8773010 airway basal cells, control, fresh, 6 airway basal cells, con…
GSM8773011 airway basal cells, control, culture, 6 airway basal cells, con…
GSM8773012 airway basal cells, control, Der p1, 6 airway basal cells, con…
GSM8773013 airway basal cells, AR, fresh, 1 airway basal cells, AR,…
GSM8773014 airway basal cells, AR, culture, 1 airway basal cells, AR,…
GSM8773015 airway basal cells, AR, Der p1, 1 airway basal cells, AR,…
GSM8773016 airway basal cells, AR, fresh, 2 airway basal cells, AR,…
GSM8773017 airway basal cells, AR, culture, 2 airway basal cells, AR,…
GSM8773018 airway basal cells, AR, Der p1, 2 airway basal cells, AR,…
GSM8773019 airway basal cells, AR, fresh, 3 airway basal cells, AR,…
GSM8773020 airway basal cells, AR, culture, 3 airway basal cells, AR,…
GSM8773021 airway basal cells, AR, Der p1, 3 airway basal cells, AR,…
GSM8773022 airway basal cells, AR, fresh, 4 airway basal cells, AR,…
GSM8773023 airway basal cells, AR, culture, 4 airway basal cells, AR,…
GSM8773024 airway basal cells, AR, Der p1, 4 airway basal cells, AR,…
GSM8773025 airway basal cells, AR, fresh, 5 airway basal cells, AR,…
GSM8773026 airway basal cells, AR, culture, 5 airway basal cells, AR,…
GSM8773027 airway basal cells, AR, Der p1, 5 airway basal cells, AR,…
GSM8773028 airway basal cells, AR, fresh, 6 airway basal cells, AR,…
GSM8773029 airway basal cells, AR, culture, 6 airway basal cells, AR,…
GSM8773030 airway basal cells, AR, Der p1, 6 airway basal cells, AR,…

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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.