← BioTransfer GEO Dataset Finder
GEO series

Gene expression profiling of A498 clear cell renal cell carcinoma cells following HIF1A and HIF2A knockdown

GSE328454 Homo sapiens (human) RNA-seq (gene expression) 12 samples Submitted 2026/07/20 Platform GPL24676
At a glance

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)
Topic
Kidney cancerThis series is part of our curated briefing on it.
Samples
12 samples: 3 × Bulk_RNA-seq_siControl vs 3 × Bulk_RNA-seq_siHIF1A vs 3 × Bulk_RNA-seq_siHIF1A_siHIF2A vs 3 × Bulk_RNA-seq_siHIF2AGroups 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 dataset investigates hypoxia-associated transcriptional regulation in clear cell renal cell carcinoma. Following the identification of hypoxia-related gene programs in malignant cells, siRNA-mediated knockdown of HIF1A, HIF2A, or both was performed in A498 cells. RNA sequencing and differential gene expression analysis were used to identify gene signatures specifically regulated by HIF1A or HIF2A.
This dataset
Open GSE328454 in finder → Find more human RNA-seq datasets → Kidney 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 GSE328454_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 PRJNA1455474 and SRA study SRP693112. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
3 × Bulk_RNA-seq_siControl vs 3 × Bulk_RNA-seq_siHIF1A vs 3 × Bulk_RNA-seq_siHIF1A_siHIF2A vs 3 × Bulk_RNA-seq_siHIF2A

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.

Samples in this study
More Kidney cancer datasets

Search all human RNA-seq datasets in GEO →

Share this dataset

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.