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Analysis of molecular mechanism of HPV18 carcinogenesis by transcriptome sequencing

GSE234041 Homo sapiens (human) RNA-seq (gene expression) 18 samples Submitted 2025/01/01 Platform GPL24676
At a glance

RNA-seq (gene expression) · human · 18 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
18 samples: 6 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.
Summary (written by the submitters)
In order to study the molecular mechanism of HPV18 carcinogenesis, we used conditional reprogramming technique to culture normal cervical epithelial cells, cervical intraepithelial Neoplasia HPV18 cells and patient-derived cervical cancer cell lines for 24 h and stimulated with estradiol for 24 h,and collected total RNA samples for mRNA sequencing (RNA-SEQ). Then, Gene expression profiling was performed using RNA-seq data from six groups of cells.
This dataset
Open GSE234041 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 GSE234041_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 PRJNA979227 and SRA study SRP440967. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
6 conditions, mostly in triplicate
normal cervical epithelial cells group, contr… ×3 normal cervical epithelial cells group, β-est… ×3 cervical intraepithelial Neoplasia HPV18 cell… ×3 cervical intraepithelial Neoplasia HPV18 cell… ×3 patient-derived cervical cancer cell group, c… ×3 patient-derived cervical cancer cell group, β… ×3

Supports a case/control comparison: 3 samples read as cases, 9 as controls.

How we read this: 6 replicated groups read from 18 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
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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.