GEO series

Transcriptome Profiling of Human Dermal Fibroblasts Treated with 4 Phosphodiesterase Inhibitors Across Multiple Dose Gradients

GSE297400 Homo sapiens (human) RNA-seq (gene expression) 199 samples Submitted 2025/05/16 Platform GPL28038

At a glance

RNA-seq (gene expression) · human · 199 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: 199 samples: 48 conditions, mostly with about 5 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 presents RNA-sequencing data from Human Primary Dermal Fibroblast, Neonatal (HDFn) cells treated with four phosphodiesterase (PDE) inhibitors—roflumilast, rolipram, cilostazol, and milrinone—across a 2-fold serial dilution range spanning from 7.8 nM to 8,000 nM. The dataset includes biological replicates for each treatment condition and dose.

Read the full summary ↓

Total RNA was extracted and sequenced on the DNBSEQ-G400 platform. The processed data includes gene-level read counts and differential gene expression results. This dataset enables dose-dependent transcriptional profiling of PDE inhibitors, providing a resource for drug response and perturbation signature analysis.

This dataset

Open GSE297400 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 GSE297400_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 PRJNA1263753 and SRA study SRP586011. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Study design

48 conditions, mostly with about 5 replicates each

Milrinone 1000 nM ×5 Milrinone 15.6 nM ×5 Milrinone 2000 nM ×5 Milrinone 250 nM ×5 Milrinone 31.3 nM ×5 Milrinone 4000 nM ×5 Milrinone 500 nM ×5 Milrinone 62.5 nM ×5 +40 more

Supports a between-group comparison across 199 samples.

How we read this: 48 replicated groups read from 199 sample titles; they account for 199 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

GSM8990210 Cilostazol 0 nM replicate 1 Cilostazol 0 nM
GSM8990211 Cilostazol 0 nM replicate 2 Cilostazol 0 nM
GSM8990212 Cilostazol 1000 nM replicate 1 Cilostazol 1000 nM
GSM8990213 Cilostazol 1000 nM replicate 2 Cilostazol 1000 nM
GSM8990214 Cilostazol 125 nM replicate 1 Cilostazol 125 nM
GSM8990215 Cilostazol 125 nM replicate 2 Cilostazol 125 nM
GSM8990216 Cilostazol 15.6 nM replicate 1 Cilostazol 15.6 nM
GSM8990217 Cilostazol 15.6 nM replicate 2 Cilostazol 15.6 nM
GSM8990218 Cilostazol 2000 nM replicate 1 Cilostazol 2000 nM
GSM8990219 Cilostazol 2000 nM replicate 2 Cilostazol 2000 nM
GSM8990220 Cilostazol 250 nM replicate 1 Cilostazol 250 nM
GSM8990221 Cilostazol 250 nM replicate 2 Cilostazol 250 nM
GSM8990222 Cilostazol 31.3 nM replicate 1 Cilostazol 31.3 nM
GSM8990223 Cilostazol 31.3 nM replicate 2 Cilostazol 31.3 nM
GSM8990224 Cilostazol 4000 nM replicate 1 Cilostazol 4000 nM
GSM8990225 Cilostazol 4000 nM replicate 2 Cilostazol 4000 nM
GSM8990226 Cilostazol 500 nM replicate 1 Cilostazol 500 nM
GSM8990227 Cilostazol 500 nM replicate 2 Cilostazol 500 nM
GSM8990228 Cilostazol 62.5 nM replicate 1 Cilostazol 62.5 nM
GSM8990229 Cilostazol 62.5 nM replicate 2 Cilostazol 62.5 nM
GSM8990230 Cilostazol 7.8 nM replicate 1 Cilostazol 7.8 nM
GSM8990231 Cilostazol 7.8 nM replicate 2 Cilostazol 7.8 nM
GSM8990232 Cilostazol 8000 nM replicate 1 Cilostazol 8000 nM
GSM8990233 Cilostazol 8000 nM replicate 2 Cilostazol 8000 nM
GSM8990234 Milrinone 0 nM replicate 1 Milrinone 0 nM
GSM8990235 Milrinone 0 nM replicate 2 Milrinone 0 nM
GSM8990236 Milrinone 0 nM replicate 3 Milrinone 0 nM
GSM8990237 Milrinone 0 nM replicate 5 Milrinone 0 nM
GSM8990238 Milrinone 1000 nM replicate 1 Milrinone 1000 nM
GSM8990239 Milrinone 1000 nM replicate 2 Milrinone 1000 nM
GSM8990240 Milrinone 1000 nM replicate 3 Milrinone 1000 nM
GSM8990241 Milrinone 1000 nM replicate 4 Milrinone 1000 nM
GSM8990242 Milrinone 1000 nM replicate 5 Milrinone 1000 nM
GSM8990243 Milrinone 125 nM replicate 1 Milrinone 125 nM
GSM8990244 Milrinone 125 nM replicate 3 Milrinone 125 nM
GSM8990245 Milrinone 125 nM replicate 5 Milrinone 125 nM
GSM8990246 Milrinone 15.6 nM replicate 1 Milrinone 15.6 nM
GSM8990247 Milrinone 15.6 nM replicate 2 Milrinone 15.6 nM
GSM8990248 Milrinone 15.6 nM replicate 3 Milrinone 15.6 nM
GSM8990249 Milrinone 15.6 nM replicate 4 Milrinone 15.6 nM

+ 159 more — browse all 199 samples with per-sample file links →

Datasets on a similar topic

GSE298908 Positionally distinct interferon-stimulated dermal immune-acting fibroblasts promote neutrophil recruitment in Sweet's syndrome [RNA-seq] 113 samples shares fibroblasts, dermal
GSE306317 A high-throughput transcriptomic profiling of fibroblasts treated with 0.0005 - 10 µM Omaveloxolone 72 samples shares fibroblasts, treated
GSE224698 Gene expression profiles of human dermal fibroblasts and human pluripotent stem cells analyzed by bulk RNA-seq 69 samples shares fibroblasts, dermal
GSE325569 Transcription analysis of primary dermal fibroblasts with different genotypes for CTGF rs9399005 SNP after irradiation or sham irradiation 51 samples shares fibroblasts, dermal
GSE281511 RNA seq of liver cancer cells treated with different concentration gradients of Thapsigargin (TG), Tunicamycin (TM), and FCCP 44 samples shares gradients, treated
GSE272460 Transcriptome analysis of pancreatic progenitor organoids (POs) carrying PDAC related mutations, treated with ERK inhibitors and depleted of AP-1 factors 40 samples shares inhibitors, treated
GSE251807 Investigation of gene expression changes in normal human dermal fibroblasts after exposure to bone marrow mesenchymal stromal cell secretome 32 samples shares fibroblasts, dermal
GSE319664 RNA-seq analysis of tumors derived from a xenograft model treated with the KDM5B inhibitors JB-157 or JB-161. 29 samples shares inhibitors, treated

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.