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GSX2 Regulates Progenitor Maturation and Regional Identity Through Transcriptional Repression in the Developing Basal Ganglia [RNA-Seq]

GSE306348 Homo sapiens (human) RNA-seq (gene expression) 21 samples Submitted 2025/09/30 Platform GPL30173
At a glance

RNA-seq (gene expression) · human · 21 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
21 samples: 7 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)
Transgenic mouse models have demonstrated the critical role of the homeodomain transcription factor Genetic-Screened Homeobox 2 (‍‍Gsx2) in the developing basal ganglia. However, the technical limitations of the existing in vivo approaches, such as progenitor heterogeneity and lack of temporal resolution, have impeded the investigation of direct regulatory targets .
Read the full summary ↓
This study engineered a Dox-inducible human embryonic stem cell (‍‍hESC) line to investigate the function of GSX2 protein in directed differentiation cultures that model developing lateral ganglionic eminence-like (LGE-like) progenitors. Transcriptomic, chromatin accessibility, and genomic binding studies revealed that GSX2: (1) binds to both high- and low-accessibility chromatin using varying binding site preferences; (‌‌‌‌2) alters chromatin accessibility largely through indirect mechanisms; (3) functions primarily as a transcriptional repressor; and (4) regulates key conserved target genes of both progenitor maturation and regional specification. These results provide insight into the key regulatory roles and targets of GSX2, thereby establishing a new tractable experimental system to investigate basal ganglia development.
This dataset
Open GSE306348 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 GSE306348_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 PRJNA1310486 and SRA study SRP612456. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
7 conditions, mostly in triplicate
H9 TRE3G 2xFLAG-GSX2 WT Day 10 ×3 H9 TRE3G 2xFLAG-GSX2 WT 12hr -Dox ×3 H9 TRE3G 2xFLAG-GSX2 WT 12hr +Dox ×3 H9 TRE3G 2xFLAG-GSX2 WT 24hr -Dox ×3 H9 TRE3G 2xFLAG-GSX2 WT 24hr +Dox ×3 H9 TRE3G 2xFLAG-GSX2 WT 48hr -Dox ×3 H9 TRE3G 2xFLAG-GSX2 WT 48hr +Dox ×3

Supports a between-group comparison across 21 samples.

How we read this: 7 replicated groups read from 21 sample titles; they account for 21 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
Datasets on a similar topic

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