GEO series

Effect of calcium oxalate microcrystals on kidney proximal tubule epithelial cell gene expression in microgravity

GSE302560 Homo sapiens (human) RNA-seq (gene expression) 144 samples Submitted 2026/06/23 Platform GPL24676

At a glance

RNA-seq (gene expression) · human · 144 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: 144 samples: 35 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: Effect of calcium oxalate microcrystals on kidney proximal tubule epithelial cell gene expression in microgravityResearch square · 2025

Summary (written by the submitters)

We evaluated the impact of spaceflight on a microphysiologic model of calcium oxalate (CaOx) kidney stone disease. Proximal tubule epithelial cells cultured as confluent microtubules were exposed to CaOx crystals with or without potassium citrate (a potential countermeasure) to determine impact on gene expression. Nine genes were differentially expressed in response to CaOx crystal exposure during spaceflight. This project presents the use of microgravity as a unique environment to study kidney pathophysiology.

Published in

Effect of calcium oxalate microcrystals on kidney proximal tubule epithelial cell gene expression in microgravity

Jones-Isaac K, Yeung CK, Bain J et al. · Research square 2025 · PMID 40678253 · doi:10.21203/rs.3.rs-6883199/v1

This dataset

Open GSE302560 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 GSE302560_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 PRJNA1291190 and SRA study SRP601299. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40678253) ↗

Study design

35 conditions, mostly in triplicate

PT10M, Control, FLIGHT, MALE, ×6 PT10M, CaOx, FLIGHT, MALE, ×6 PT10M, KCit, FLIGHT, MALE, ×6 PT6F, Control, FLIGHT, FEMALE, ×6 PT6F, CaOx, FLIGHT, FEMALE, ×6 PT6F, KCit, FLIGHT, FEMALE, ×6 PT10M, Control, GROUND, MALE, ×6 PT10M, CaOx, GROUND, MALE, ×6 +27 more

Supports a between-group comparison across 144 samples.

How we read this: 35 replicated groups read from 144 sample titles; they account for 144 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

GSM9106062 PT10M, Control, FLIGHT, MALE, replicate 1 PT10M, Control, FLIGHT,…
GSM9106063 PT10M, Control, FLIGHT, MALE, replicate 2 PT10M, Control, FLIGHT,…
GSM9106064 PT10M, Control, FLIGHT, MALE, replicate 3 PT10M, Control, FLIGHT,…
GSM9106065 PT10M, CaOx, FLIGHT, MALE, replicate 1 PT10M, CaOx, FLIGHT, MA…
GSM9106066 PT10M, CaOx, FLIGHT, MALE, replicate 2 PT10M, CaOx, FLIGHT, MA…
GSM9106067 PT10M, CaOx, FLIGHT, MALE, replicate 3 PT10M, CaOx, FLIGHT, MA…
GSM9106068 PT10M, KCit, FLIGHT, MALE, replicate 1 PT10M, KCit, FLIGHT, MA…
GSM9106069 PT10M, KCit, FLIGHT, MALE, replicate 2 PT10M, KCit, FLIGHT, MA…
GSM9106070 PT10M, KCit, FLIGHT, MALE, replicate 3 PT10M, KCit, FLIGHT, MA…
GSM9106071 PT5F, Control, FLIGHT, FEMALE, replicate 1 PT5F, Control, FLIGHT, …
GSM9106072 PT5F, Control, FLIGHT, FEMALE, replicate 2 PT5F, Control, FLIGHT, …
GSM9106073 PT5F, Control, FLIGHT, FEMALE, replicate 3 PT5F, Control, FLIGHT, …
GSM9106074 PT6F, Control, FLIGHT, FEMALE, replicate 1 PT6F, Control, FLIGHT, …
GSM9106075 PT6F, Control, FLIGHT, FEMALE, replicate 2 PT6F, Control, FLIGHT, …
GSM9106076 PT6F, Control, FLIGHT, FEMALE, replicate 3 PT6F, Control, FLIGHT, …
GSM9106077 PT7M, Control, FLIGHT, MALE, replicate 1 PT7M, Control, FLIGHT, …
GSM9106078 PT7M, Control, FLIGHT, MALE, replicate 2 PT7M, Control, FLIGHT, …
GSM9106079 PT7M, Control, FLIGHT, MALE, replicate 3 PT7M, Control, FLIGHT, …
GSM9106080 PT5F, CaOx, FLIGHT, FEMALE, replicate 1 PT5F, CaOx, FLIGHT, FEM…
GSM9106081 PT5F, CaOx, FLIGHT, FEMALE, replicate 2 PT5F, CaOx, FLIGHT, FEM…
GSM9106082 PT5F, CaOx, FLIGHT, FEMALE, replicate 3 PT5F, CaOx, FLIGHT, FEM…
GSM9106083 PT6F, CaOx, FLIGHT, FEMALE, replicate 1 PT6F, CaOx, FLIGHT, FEM…
GSM9106084 PT6F, CaOx, FLIGHT, FEMALE, replicate 2 PT6F, CaOx, FLIGHT, FEM…
GSM9106085 PT6F, CaOx, FLIGHT, FEMALE, replicate 3 PT6F, CaOx, FLIGHT, FEM…
GSM9106086 PT7M, CaOx, FLIGHT, MALE, replicate 1 PT7M, CaOx, FLIGHT, MAL…
GSM9106087 PT7M, CaOx, FLIGHT, MALE, replicate 2 PT7M, CaOx, FLIGHT, MAL…
GSM9106088 PT7M, CaOx, FLIGHT, MALE, replicate 3 PT7M, CaOx, FLIGHT, MAL…
GSM9106089 PT5F, KCit, FLIGHT, FEMALE, replicate 1 PT5F, KCit, FLIGHT, FEM…
GSM9106090 PT5F, KCit, FLIGHT, FEMALE, replicate 2 PT5F, KCit, FLIGHT, FEM…
GSM9106091 PT5F, KCit, FLIGHT, FEMALE, replicate 3 PT5F, KCit, FLIGHT, FEM…
GSM9106092 PT6F, KCit, FLIGHT, FEMALE, replicate 1 PT6F, KCit, FLIGHT, FEM…
GSM9106093 PT6F, KCit, FLIGHT, FEMALE, replicate 2 PT6F, KCit, FLIGHT, FEM…
GSM9106094 PT6F, KCit, FLIGHT, FEMALE, replicate 3 PT6F, KCit, FLIGHT, FEM…
GSM9106095 PT7M, KCit, FLIGHT, MALE, replicate 1 PT7M, KCit, FLIGHT, MAL…
GSM9106096 PT7M, KCit, FLIGHT, MALE, replicate 2 PT7M, KCit, FLIGHT, MAL…
GSM9106097 PT7M, KCit, FLIGHT, MALE, replicate 3 PT7M, KCit, FLIGHT, MAL…
GSM9106098 PT6F, Control, FLIGHT, FEMALE, replicate 4 PT6F, Control, FLIGHT, …
GSM9106099 PT6F, Control, FLIGHT, FEMALE, replicate 5 PT6F, Control, FLIGHT, …
GSM9106100 PT6F, Control, FLIGHT, FEMALE, replicate 6 PT6F, Control, FLIGHT, …
GSM9106101 PT6F, CaOx, FLIGHT, FEMALE, replicate 4 PT6F, CaOx, FLIGHT, FEM…

+ 104 more — browse all 144 samples with per-sample file links →

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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.