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Effect of adenoviral E1A on oxaliplatin response in oxaliplatin-sensitive and resistant human colorectal cancer HCT116 cells

GSE304295 Homo sapiens (human) RNA-seq (gene expression) 24 samples Submitted 2025/11/14 Platform GPL34281
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
Colorectal cancerThis series is part of our curated briefing on it.
Samples
24 samples: 8 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.
Paper
Transcriptomic and Cytogenetic Analysis of Oxaliplatin-Resistant Colorectal Adenocarcinoma HCT116 Cells to Identify Markers Associated with Platinum ResistanceInternational journal of molecular sciences · 2025
Summary (written by the submitters)
Resistance to chemotherapy drugs, including oxaliplatin, remains a major challenge in the treatment of colorectal cancer, often leading to treatment failure and poor patient outcomes. Overcoming chemoresistance by sensitizing tumor cells represents a critical therapeutic goal. Adenoviral early region 1A (E1A) has been proposed as a promising gene therapy agent capable of modulating cellular pathways to enhance sensitivity to chemotherapeutic agents.
Read the full summary ↓
This dataset contains RNA-seq profiling of human colorectal cancer cell lines that are either oxaliplatin-sensitive (HCT116) or oxaliplatin-resistant (HCT116 oxpl-R), treated with oxaliplatin, in the context of doxycycline-induced adenoviral E1A expression. The experiment includes eight conditions: untreated controls, E1A expression alone, oxaliplatin treatment alone, and combined E1A expression with oxaliplatin treatment, each in both sensitive and resistant cell lines. The comprehensive experimental design enables the dataset to be divided into three independent analyses: A) Comparison of baseline transcriptomic profiles between oxaliplatin-sensitive and resistant cells (conditions 1 and 5); B) Investigation of the transcriptional response to oxaliplatin in sensitive and resistant cells (conditions 1, 3, 5, and 7); C) Evaluation of the impact of adenoviral E1A expression on the transcriptomes of sensitive and resistant cells alone (conditions 1, 2, 5, and 6) and in combination with oxaliplatin treatment (all eight conditions); This dataset provides valuable insights into the molecular mechanisms underlying oxaliplatin resistance and the potential role of E1A gene therapy in sensitizing colorectal cancer cells to chemotherapy.
Published in
Transcriptomic and Cytogenetic Analysis of Oxaliplatin-Resistant Colorectal Adenocarcinoma HCT116 Cells to Identify Markers Associated with Platinum Resistance
Morshneva A, Gnedina O, Fedotova K et al. · International journal of molecular sciences 2025 · PMID 41009436 · doi:10.3390/ijms26188869
This dataset
Open GSE304295 in finder → Find more human RNA-seq datasets → Colorectal 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 GSE304295_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 PRJNA1300304 and SRA study SRP605777. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41009436) ↗
Study design
8 conditions, mostly in triplicate
HCT116 control, biol ×3 HCT116 E1A, biol ×3 HCT116 oxaliplatin, biol ×3 HCT116 E1A + oxaliplatin, biol ×3 HCT116 oxpl-R, biol ×3 HCT116 oxpl-R E1A, biol ×3 HCT116 oxpl-R oxaliplatin, biol ×3 HCT116 oxpl-R E1A + oxaliplatin, biol ×3

Supports a between-group comparison across 24 samples.

How we read this: 8 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 Colorectal 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.