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Integrated Transcriptomic and Functional Analysis Reveals Selective Cytotoxicity and Oncogene Suppression Induced by Cinnamon Essential Oil in Cervical Cancer Cells

GSE311189 Homo sapiens (human) RNA-seq (gene expression) 24 samples Submitted 2026/05/05 Platform GPL24676
At a glance

RNA-seq (gene expression) · human · 24 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)
Topic
Cervical cancerThis series is part of our curated briefing on it.
Samples
24 samples: 6 conditions, mostly with about 4 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)
This study aimed to evaluate the effect of cinnamon (Cinnamomum zeylanicum) essential oil (CEO) on cervical cancer cell lines (HeLa and SiHa) and an immortalized human keratinocyte cell line (HaCaT) by analyzing its impact on gene expression modulation. Total RNA sequencing was performed using the Illumina NovaSeq 6000 platform by Novogene Bioinformatics Technology Co., Ltd.
Read the full summary ↓
(Beijing, China), with four independent replicates for each cell model. Bioinformatics analysis was conducted using R (v4.3.1), RStudio (v2023.09.1+494), and the open-source Galaxy platform (https://usegalaxy.org; accessed on February 5, 2025). Quality control was performed with FastQC (v0.74+galaxy0). Subsequently, reads were processed with the Rsubread package (v2.14.2), trimmed, and aligned to the human reference genome (GRCh38.p14 v46). The resulting BAM files were used for read counting with FeatureCounts (v2.0.3). Differential expression analysis was carried out using the DESeq2 package for R (v1.42.0). Normalization of gene expression was performed using DESeq2’s median-of-ratios method (median ratio of gene counts relative to the geometric mean per gene). Genes with an adjusted p-value ≤ 0.05 and |Log2FC| ≥ 2 were considered differentially expressed genes (DEGs). Transcriptomic analysis revealed significant upregulation of genes involved in cellular stress responses, DNA damage repair, and protein synthesis. DEGs were enriched in apoptosis, cell cycle regulation, and p53 signaling pathways. Additionally, CEO treatment led to suppression of genes associated with oxidative phosphorylation and cell cycle progression, with HeLa cells showing the highest sensitivity.
This dataset
Open GSE311189 in finder → Find more human RNA-seq datasets → Cervical cancer landscape →
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 GSE311189_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 PRJNA1368772 and SRA study SRP648761. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
6 conditions, mostly with about 4 replicates each
HCTCAN ×4 HCTDMSO ×4 HLCAN ×4 HLDMSO ×4 SHCAN ×4 SHDMSO ×4

Supports a between-group comparison across 24 samples.

How we read this: 6 replicated groups read from 24 sample titles; they account for 24 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
More Cervical cancer datasets

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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.