← BioTransfer GEO Dataset Finder
GEO series

Effect of PHGDH knockdown on gene expression in human immortalized keratinocytes (HaCaT cells)

GSE228865 Homo sapiens (human) RNA-seq (gene expression) 12 samples Submitted 2026/02/26 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)
Samples
12 samples: 3 × HaCaT cells, Control-siRNA vs 3 × HaCaT cells, Control-siRNA+Mix vs 3 × HaCaT cells, PHGDH-siRNA vs 3 × HaCaT cells, PHGDH-siRNA+MixGroups 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
Serine deficiency exacerbates psoriatic skin inflammation by regulating S-adenosyl methionine-dependent DNA methylation and NF-κB signalling activation in keratinocytesJournal of the European Academy of Dermatology and Venereology : JEADV · 2024
Summary (written by the submitters)
To investigate the role of PHGDH in the regulation of psoriatic keratinocyte inflammation, we challenged HaCaT cells with PHGDH-siRNA and stimulated with IL-17A, IL-22, IL-1α, OSM and TNFα (mix) coctails. We then performed gene expresssion profiling analysis using data obtained from RNA-seq of 4 groups of samples
Published in
Serine deficiency exacerbates psoriatic skin inflammation by regulating S-adenosyl methionine-dependent DNA methylation and NF-κB signalling activation in keratinocytes
Meng Q, Liu Y, Yao L et al. · Journal of the European Academy of Dermatology and Venereology : JEADV 2024 · PMID 37669859 · doi:10.1111/jdv.19492
This dataset
Open GSE228865 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 GSE228865_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 PRJNA951753 and SRA study SRP430660. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 37669859) ↗
Study design
3 × HaCaT cells, Control-siRNA vs 3 × HaCaT cells, Control-siRNA+Mix vs 3 × HaCaT cells, PHGDH-siRNA vs 3 × HaCaT cells, PHGDH-siRNA+Mix

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
Datasets on a similar topic

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.