Cell passage number: an intrinsic factor influencing the reproducibility of cell experiments
RNA-seq (gene expression) · mouse · 20 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
- Mus musculus (mouse)
- Samples
- 20 samples: 10 conditions, mostly in duplicateGroups 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
- Cell passage number drives transcriptomic drift as an overlooked factor in experimental reproducibilityScientific reports · 2025
Read the full summary ↓
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.
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.
Supplementary files
The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE308793_RAW.tar (it can run to tens of gigabytes).
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.
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 PRJNA1332728 and SRA study SRP624982. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 20 samples.
How we read this: 10 replicated groups read from 20 sample titles; they account for 20 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.
- GSM9253260 ACHN cells, passage 3, rep1 ACHN cells, passage 3,
- GSM9253261 ACHN cells, passage 3, rep2 ACHN cells, passage 3,
- GSM9253262 ACHN cells, passage 10, rep1 ACHN cells, passage 10,
- GSM9253263 ACHN cells, passage 10, rep2 ACHN cells, passage 10,
- GSM9253264 ACHN cells, passage 17, rep1 ACHN cells, passage 17,
- GSM9253265 ACHN cells, passage 17, rep2 ACHN cells, passage 17,
- GSM9253266 ACHN cells, passage 24, rep1 ACHN cells, passage 24,
- GSM9253267 ACHN cells, passage 24, rep2 ACHN cells, passage 24,
- GSM9253268 ACHN cells, passage 39, rep1 ACHN cells, passage 39,
- GSM9253269 ACHN cells, passage 39, rep2 ACHN cells, passage 39,
- GSM9253270 Renca cells, passage 3, rep1 Renca cells, passage 3,
- GSM9253271 Renca cells, passage 3, rep2 Renca cells, passage 3,
- GSM9253272 Renca cells, passage 10, rep1 Renca cells, passage 10,
- GSM9253273 Renca cells, passage 10, rep2 Renca cells, passage 10,
- GSM9253274 Renca cells, passage 17, rep1 Renca cells, passage 17,
- GSM9253275 Renca cells, passage 17, rep2 Renca cells, passage 17,
- GSM9253276 Renca cells, passage 24, rep1 Renca cells, passage 24,
- GSM9253277 Renca cells, passage 24, rep2 Renca cells, passage 24,
- GSM9253278 Renca cells, passage 39, rep1 Renca cells, passage 39,
- GSM9253279 Renca cells, passage 39, rep2 Renca cells, passage 39,
- GSE246923 Opposing tumor cell-intrinsic and -extrinsic roles of the IRF1 transcription factor in anti-tumor immunity 49 samples shares intrinsic, factor
- GSE305855 Casein kinase 1δ/ε inhibition suppresses CLL through cell-intrinsic and microenvironmental mechanisms [RNA-Seq] 42 samples shares intrinsic
- GSE294355 Dual function of DOT1L suppresses tumor intrinsic immunogenicity in Hepatocellular carcinoma [RNA-seq] 36 samples shares intrinsic
- GSE324714 Acquired genetic and cell state changes in IDH-mutant glioma progression [coculture experiments] 16 samples shares experiments
- GSE267542 Tumor intrinsic METTL5 induces immune resistance in ovarian cancer by suppressing ferroptosis 18 samples shares intrinsic
- GSE250467 Oncohistone H3.3K27M-driven CREB5/ID1 Axis Mediates the Malignant Cell States of Diffuse Intrinsic Pontine Glioma (DIPG) 52 samples shares intrinsic
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.