GEO series

RNA sequencing of human brain organoids to evaluate sex-specific and opto-FGFR-mediated responses to Simplified 5 Ion GCR Simulation

GSE309755 Homo sapiens (human) RNA-seq (gene expression) 66 samples Submitted 2025/12/08 Platform GPL24676

At a glance

RNA-seq (gene expression) · human · 66 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: 66 samples: 22 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.

Summary (written by the submitters)

This study aims to characterize transcriptomic responses to Simplified 5 Ion GCR Simulation (simGCRsim) in human brain organoids derived from hiPSCs. Two independent RNA-seq experiments were conducted. The first set compared male- and female-derived organoids to evaluate sex-specific transcriptional responses to GCR. The second set assessed organoids derived from i) male hiPSCs expressing optogenetically-controlled FGFR (opto-FGFR) or mock constructs to explore FGFR signaling as a potential countermeasure and ii) one female hiPSC line (SC2131), with or without GCR exposure.

Read the full summary ↓

Together, these datasets provide insight into both intrinsic sex differences and FGFR-dependent protective mechanisms in human neural tissues in the context of space radiation exposure.

This dataset

Open GSE309755 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 GSE309755_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 PRJNA1336937 and SRA study SRP630215. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Study design

22 conditions, mostly in triplicate

RNA-seq of male brain organoid derived from S… ×3 RNA-seq of male brain organoid derived from S… ×3 RNA-seq of male brain organoid derived from C… ×3 RNA-seq of male brain organoid derived from C… ×3 RNA-seq of male brain organoid derived from B… ×3 RNA-seq of male brain organoid derived from B… ×3 RNA-seq of male brain organoid derived from A… ×3 RNA-seq of male brain organoid derived from A… ×3 +14 more

Supports a between-group comparison across 66 samples.

How we read this: 22 replicated groups read from 66 sample titles; they account for 66 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

GSM9278514 RNA-seq of male brain organoid derived from SC1015 cell lines without simGCRsim #1 RNA-seq of male brain o…
GSM9278515 RNA-seq of male brain organoid derived from SC1015 cell lines without simGCRsim #2 RNA-seq of male brain o…
GSM9278516 RNA-seq of male brain organoid derived from SC1015 cell lines without simGCRsim #3 RNA-seq of male brain o…
GSM9278517 RNA-seq of male brain organoid derived from SC1015 cell lines with simGCRsim #1 RNA-seq of male brain o…
GSM9278518 RNA-seq of male brain organoid derived from SC1015 cell lines with simGCRsim #2 RNA-seq of male brain o…
GSM9278519 RNA-seq of male brain organoid derived from SC1015 cell lines with simGCRsim #3 RNA-seq of male brain o…
GSM9278520 RNA-seq of male brain organoid derived from CS25 cell lines without simGCRsim #1 RNA-seq of male brain o…
GSM9278521 RNA-seq of male brain organoid derived from CS25 cell lines without simGCRsim #2 RNA-seq of male brain o…
GSM9278522 RNA-seq of male brain organoid derived from CS25 cell lines without simGCRsim #3 RNA-seq of male brain o…
GSM9278523 RNA-seq of male brain organoid derived from CS25 cell lines with simGCRsim #1 RNA-seq of male brain o…
GSM9278524 RNA-seq of male brain organoid derived from CS25 cell lines with simGCRsim #2 RNA-seq of male brain o…
GSM9278525 RNA-seq of male brain organoid derived from CS25 cell lines with simGCRsim #3 RNA-seq of male brain o…
GSM9278526 RNA-seq of male brain organoid derived from BC1 cell lines without simGCRsim #1 RNA-seq of male brain o…
GSM9278527 RNA-seq of male brain organoid derived from BC1 cell lines without simGCRsim #2 RNA-seq of male brain o…
GSM9278528 RNA-seq of male brain organoid derived from BC1 cell lines without simGCRsim #3 RNA-seq of male brain o…
GSM9278529 RNA-seq of male brain organoid derived from BC1 cell lines with simGCRsim #1 RNA-seq of male brain o…
GSM9278530 RNA-seq of male brain organoid derived from BC1 cell lines with simGCRsim #2 RNA-seq of male brain o…
GSM9278531 RNA-seq of male brain organoid derived from BC1 cell lines with simGCRsim #3 RNA-seq of male brain o…
GSM9278532 RNA-seq of male brain organoid derived from ApoE cell lines without simGCRsim #1 RNA-seq of male brain o…
GSM9278533 RNA-seq of male brain organoid derived from ApoE cell lines without simGCRsim #2 RNA-seq of male brain o…
GSM9278534 RNA-seq of male brain organoid derived from ApoE cell lines without simGCRsim #3 RNA-seq of male brain o…
GSM9278535 RNA-seq of male brain organoid derived from ApoE cell lines with simGCRsim #1 RNA-seq of male brain o…
GSM9278536 RNA-seq of male brain organoid derived from ApoE cell lines with simGCRsim #2 RNA-seq of male brain o…
GSM9278537 RNA-seq of male brain organoid derived from ApoE cell lines with simGCRsim #3 RNA-seq of male brain o…
GSM9278538 RNA-seq of female brain organoid derived from H9 cell lines without simGCRsim #1 RNA-seq of female brain…
GSM9278539 RNA-seq of female brain organoid derived from H9 cell lines without simGCRsim #2 RNA-seq of female brain…
GSM9278540 RNA-seq of female brain organoid derived from H9 cell lines without simGCRsim #3 RNA-seq of female brain…
GSM9278541 RNA-seq of female brain organoid derived from H9 cell lines with simGCRsim #1 RNA-seq of female brain…
GSM9278542 RNA-seq of female brain organoid derived from H9 cell lines with simGCRsim #2 RNA-seq of female brain…
GSM9278543 RNA-seq of female brain organoid derived from H9 cell lines with simGCRsim #3 RNA-seq of female brain…
GSM9278544 RNA-seq of male brain organoid derived from KOLF2.1J cell lines without simGCRsim #1 RNA-seq of male brain o…
GSM9278545 RNA-seq of male brain organoid derived from KOLF2.1J cell lines without simGCRsim #2 RNA-seq of male brain o…
GSM9278546 RNA-seq of male brain organoid derived from KOLF2.1J cell lines without simGCRsim #3 RNA-seq of male brain o…
GSM9278547 RNA-seq of male brain organoid derived from KOLF2.1J cell lines with simGCRsim #1 RNA-seq of male brain o…
GSM9278548 RNA-seq of male brain organoid derived from KOLF2.1J cell lines with simGCRsim #2 RNA-seq of male brain o…
GSM9278549 RNA-seq of male brain organoid derived from KOLF2.1J cell lines with simGCRsim #3 RNA-seq of male brain o…
GSM9278550 RNA-seq of male brain organoid derived from SC1014 cell lines without simGCRsim #1 RNA-seq of male brain o…
GSM9278551 RNA-seq of male brain organoid derived from SC1014 cell lines without simGCRsim #2 RNA-seq of male brain o…
GSM9278552 RNA-seq of male brain organoid derived from SC1014 cell lines without simGCRsim #3 RNA-seq of male brain o…
GSM9278553 RNA-seq of male brain organoid derived from SC1014 cell lines with simGCRsim #1 RNA-seq of male brain o…

+ 26 more — browse all 66 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.