GEO series

Baseline Gene Expression in Human Derived Cell Lines

GSE288929 Homo sapiens (human) RNA-seq (gene expression) 180 samples Submitted 2025/02/11 Platform GPL16791

At a glance

RNA-seq (gene expression) · human · 180 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: 180 samples: 60 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: TempO-seq and RNA-seq gene expression levels are highly correlated for most genes: A comparison using 39 human cell linesPloS one · 2025

Summary (written by the submitters)

Many research organizations are exploring the use of high-throughput profiling (HTP) assays such as transcriptomics and image-based phenotypic profiling for in vitro bioactivity screening and hazard evaluation of chemicals. HTP assays can be used to characterize the response of many human-derived cell types to chemicals. However, no cell-based in vitro model will express all the potential molecular targets and pathways that are present in the human body that could be perturbed, resulting in toxicity.

Read the full summary ↓

Therefore, an envisioned approach for the use of HTP assays in chemical bioactivity screening involves panels of cell lines that express complementary (partially non-overlapping) sets of molecular targets. In this study, baseline gene expression in 53 different human-derived cell lines was characterized using the TempO-Seq human whole transcriptome assay. The cell line set included 36 human cancer-derived cell lines and 17 engineered or spontanously immortalized human cell lines. The baseline gene expression data can inform what set(s) of molecular targets are expressed across the cell line collection and inform researchers regarding the choice of cell lines for chemical screening studies.

Published in

TempO-seq and RNA-seq gene expression levels are highly correlated for most genes: A comparison using 39 human cell lines

Word LJ, Willis CM, Judson RS et al. · PloS one 2025 · PMID 40344165 · doi:10.1371/journal.pone.0320862

This dataset

Open GSE288929 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 GSE288929_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 PRJNA1220047 and SRA study SRP562002. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40344165) ↗

Study design

60 conditions, mostly in triplicate

HepaRG (2D), Phase 1, ×3 HepaRG (3D), Phase 1, ×3 TeloHAEC, Phase 1, ×3 TIME, Phase 1, ×3 Ker-CT, Phase 1, ×3 ASC52Telo, Phase 1, ×3 RPTEC/TERT1, Phase 1, ×3 HSAEC1-KT, Phase 1, ×3 +52 more

Supports a between-group comparison across 180 samples.

How we read this: 60 replicated groups read from 180 sample titles; they account for 180 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

GSM8779008 HepaRG (2D), Phase 1, Replicate 1 HepaRG (2D), Phase 1,
GSM8779009 HepaRG (2D), Phase 1, Replicate 2 HepaRG (2D), Phase 1,
GSM8779010 HepaRG (2D), Phase 1, Replicate 3 HepaRG (2D), Phase 1,
GSM8779011 HepaRG (3D), Phase 1, Replicate 1 HepaRG (3D), Phase 1,
GSM8779012 HepaRG (3D), Phase 1, Replicate 2 HepaRG (3D), Phase 1,
GSM8779013 HepaRG (3D), Phase 1, Replicate 3 HepaRG (3D), Phase 1,
GSM8779014 TeloHAEC, Phase 1, Replicate 1 TeloHAEC, Phase 1,
GSM8779015 TeloHAEC, Phase 1, Replicate 2 TeloHAEC, Phase 1,
GSM8779016 TeloHAEC, Phase 1, Replicate 3 TeloHAEC, Phase 1,
GSM8779017 TIME, Phase 1, Replicate 1 TIME, Phase 1,
GSM8779018 TIME, Phase 1, Replicate 2 TIME, Phase 1,
GSM8779019 TIME, Phase 1, Replicate 3 TIME, Phase 1,
GSM8779020 Ker-CT, Phase 1, Replicate 1 Ker-CT, Phase 1,
GSM8779021 Ker-CT, Phase 1, Replicate 2 Ker-CT, Phase 1,
GSM8779022 Ker-CT, Phase 1, Replicate 3 Ker-CT, Phase 1,
GSM8779023 ASC52Telo, Phase 1, Replicate 1 ASC52Telo, Phase 1,
GSM8779024 ASC52Telo, Phase 1, Replicate 2 ASC52Telo, Phase 1,
GSM8779025 ASC52Telo, Phase 1, Replicate 3 ASC52Telo, Phase 1,
GSM8779026 RPTEC/TERT1, Phase 1, Replicate 1 RPTEC/TERT1, Phase 1,
GSM8779027 RPTEC/TERT1, Phase 1, Replicate 2 RPTEC/TERT1, Phase 1,
GSM8779028 RPTEC/TERT1, Phase 1, Replicate 3 RPTEC/TERT1, Phase 1,
GSM8779029 HSAEC1-KT, Phase 1, Replicate 1 HSAEC1-KT, Phase 1,
GSM8779030 HSAEC1-KT, Phase 1, Replicate 2 HSAEC1-KT, Phase 1,
GSM8779031 HSAEC1-KT, Phase 1, Replicate 3 HSAEC1-KT, Phase 1,
GSM8779032 hTERT-HME1, Phase 1, Replicate 1 hTERT-HME1, Phase 1,
GSM8779033 hTERT-HME1, Phase 1, Replicate 2 hTERT-HME1, Phase 1,
GSM8779034 hTERT-HME1, Phase 1, Replicate 3 hTERT-HME1, Phase 1,
GSM8779035 hTERT-RPE1, Phase 1, Replicate 1 hTERT-RPE1, Phase 1,
GSM8779036 hTERT-RPE1, Phase 1, Replicate 2 hTERT-RPE1, Phase 1,
GSM8779037 hTERT-RPE1, Phase 1, Replicate 3 hTERT-RPE1, Phase 1,
GSM8779038 BJ-5ta, Phase 1, Replicate 1 BJ-5ta, Phase 1,
GSM8779039 BJ-5ta, Phase 1, Replicate 2 BJ-5ta, Phase 1,
GSM8779040 BJ-5ta, Phase 1, Replicate 3 BJ-5ta, Phase 1,
GSM8779041 A549, Phase 1, Replicate 1 A549, Phase 1,
GSM8779042 A549, Phase 1, Replicate 2 A549, Phase 1,
GSM8779043 A549, Phase 1, Replicate 3 A549, Phase 1,
GSM8779044 ARPE-19, Phase 1, Replicate 1 ARPE-19, Phase 1,
GSM8779045 ARPE-19, Phase 1, Replicate 2 ARPE-19, Phase 1,
GSM8779046 ARPE-19, Phase 1, Replicate 3 ARPE-19, Phase 1,
GSM8779047 U-2 OS, Phase 1, Replicate 1 U-2 OS, Phase 1,

+ 140 more — browse all 180 samples with per-sample file links →

Datasets on a similar topic

GSE327944 Effects of adenovirus mediated GLA expression on gene expression of hiPSC-derived ventricular cardiomyocytes from control and Fabri Disease Lines 12 samples shares derived, lines
GSE285203 Transcriptome analyses of human corneal endothelial cell lines derived from patients with Fuchs Endothelial Corneal Dystrophy 11 samples shares derived, lines
GSE263588 Comprehensive transcriptomic profiling of glioblastoma patient-derived primary tumor cell lines using bulk RNA-sequencing 49 samples shares derived, lines
GSE262419 Informing Hazard Identification and Risk Characterization of Environmental Chemicals by Combining Transcriptomic and Functional Data from Human Induced Pluripotent Stem Cell-Derived Cardiomyocytes 4558 samples shares derived
GSE226482 Single cell RNA sequencing of spinal motor neurons and interneurons differentiated from isogenic FUS and TARDBP human induced pluripotent stem cell lines harbouring ALS-causative mutations 1415 samples shares lines
GSE274620 Temporal multiomics gene expression data across human embryonic stem cell derived cardiomyocyte differentiation [RNA-seq] 20 samples shares derived
GSE273995 Cell-intrinsic platinum response and associated genetic and gene expression signatures in ovarian cancer cell lines and isogenic models 36 samples shares lines
GSE274006 Cell-intrinsic platinum response and associated genetic and gene expression signatures in ovarian cancer cell lines and isogenic models [isogenic models] 33 samples shares lines

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.