Limited response of primary nasal epithelial cells to Bordetella pertussis infection
RNA-seq (gene expression) · human · 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
- Homo sapiens (human)
- Samples
- 12 samples: 3 × hNECs, uninfected, 24h, vs 3 × hNECs, WT-infected, 24h, vs 3 × hNECs, delta_bteA_infected, 24h, vs 3 × bteA_infected, 24h,Groups 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
- Limited response of primary nasal epithelial cells to Bordetella pertussis infectionMicrobiology spectrum · 2025
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.
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.
Supplementary files
The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE288608_RAW.tar (it can run to tens of gigabytes).
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.
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 PRJNA1214286 and SRA study SRP559109. Searching any of these in the dataset finder brings you back here.
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.
- GSM8770963 hNECs, uninfected, 24h, rep1 hNECs, uninfected, 24h,
- GSM8770964 hNECs, uninfected, 24h, rep2 hNECs, uninfected, 24h,
- GSM8770965 hNECs, uninfected, 24h, rep3 hNECs, uninfected, 24h,
- GSM8770966 hNECs, WT-infected, 24h, rep1 hNECs, WT-infected, 24h,
- GSM8770967 hNECs, WT-infected, 24h, rep2 hNECs, WT-infected, 24h,
- GSM8770968 hNECs, WT-infected, 24h, rep3 hNECs, WT-infected, 24h,
- GSM8770969 hNECs, delta_bteA_infected, 24h, rep1 hNECs, delta_bteA_infec…
- GSM8770970 hNECs, delta_bteA_infected, 24h, rep2 hNECs, delta_bteA_infec…
- GSM8770971 hNECs, delta_bteA_infected, 24h, rep3 hNECs, delta_bteA_infec…
- GSM8770972 hNECs, delta_bteA::bteA_infected, 24h, rep1 bteA_infected, 24h,
- GSM8770973 hNECs, delta_bteA::bteA_infected, 24h, rep2 bteA_infected, 24h,
- GSM8770974 hNECs, delta_bteA::bteA_infected, 24h, rep3 bteA_infected, 24h,
- GSE310241 Mucosal inflammation and pre-existing antibodies define protection and disease outcomes in human Bordetella pertussis challenge 414 samples shares bordetella, pertussis
- GSE292944 Culture Media Strongly Influences Primary Human Bronchial Epithelial Cells' Transcriptomic Response to Ozone Exposure 24 samples shares epithelial, primary
- GSE238235 The impact of vaping on adolescent lung function and nasal epithelial gene expression [RNA-seq] 48 samples shares epithelial, nasal
- GSE276503 Myeloid-derived IL1B drives epithelial and stromal cell remodeling during chronic rhinosinusitis and nasal polyps [scRNA-seq] 33 samples shares epithelial, nasal
- GSE235711 Immune-Epithelial Interactions and Tissue Remodeling in the Inflammatory Respiratory Nasal Tract [scRNA-seq] 20 samples shares epithelial, nasal
- GSE287215 Bulk RNA-Seq of primary human bronchial epithelial cells after transfection with different Cas9 formats 17 samples shares epithelial, primary
- GSE241292 SARS-CoV-2-infected human nasal epithelial air-liquid interface cultures 16 samples shares epithelial, nasal
- GSE238079 Characterizing immune signatures of seasonal coronaviruses HCoV-229E and -OC43 in human nasal airway epithelial cells 10 samples shares epithelial, nasal
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.