GEO series

RAI1 safeguards fidelity and tempo of human neurodevelopmental gene expression [RNA-seq]

GSE336167 Homo sapiens (human) Single-cell RNA-seq 36 samples Submitted 2026/07/08 Platform GPL34284

At a glance

Single-cell RNA-seq · human · 36 samples

What it is: Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart. Read from the summary: GEO's own type field only says 'expression profiling by sequencing', so confirm it in the paper.
Organism: Homo sapiens (human)
Samples: 36 samples: 9 conditions, mostly with about 4 replicates eachGroups 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)

Human brain development proceeds on an unusually long timeline, fostering the species' cognitive advantages. Retinoic Acid Induced 1 (RAI1) gene encodes a nucleosome-binding protein haploinsufficient in Smith–Magenis Syndrome (SMS), a neurodevelopmental disorder characterized by cognitive deficits with autistic features. However, the role of RAI1 in human neurodevelopment remains unexplored experimentally.

Read the full summary ↓

Here, we generated isogenic heterozygous and homozygous RAI1 loss-of-function human embryonic stem cell lines and interrogated the roles of RAI1 in neurodevelopmental gene regulation. A longitudinal transcriptome study during in vitro cortical development revealed that RAI1 deficiency accelerates developmental transcriptome progression, as indicated by the induction of synaptic genes. Single-cell RNA-seq analysis revealed that RAI1-deficient neuroprogenitors acquire a transient mesoderm-like gene expression signature followed by pro-neuronal maturation gene expression in postmitotic neurons. Unexpectedly, the developmental acceleration signature was exacerbated during NGN2-induced excitatory neuron differentiation, suggesting functional interplay between RAI1 and NGN2-driven programs. Together, these results identify RAI1 as a suppressor of the mesodermal lineage program and as a novel brake that slows the tempo of human neurodevelopmental gene expression.

This dataset

Open GSE336167 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 GSE336167_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: Single-cell studies usually ship their counts as 10x files (matrix.mtx, barcodes.tsv, features.tsv), an .h5 file, or an .rds / .h5ad object that Seurat or Scanpy can open. Look for those among the supplementary files.

Also filed as BioProject PRJNA1480798 and SRA study SRP711594. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Study design

9 conditions, mostly with about 4 replicates each

WT_D0 ×4 HET_D0 ×4 KO_D0 ×4 WT_D3 ×4 HET_D3 ×4 KO_D3 ×4 WT_D7 ×4 HET_D7 ×4 +1 more

Supports a between-group comparison across 36 samples.

How we read this: 9 replicated groups read from 36 sample titles; they account for 36 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

GSM9829341 WT_D0_rep1 WT_D0
GSM9829342 WT_D0_rep2 WT_D0
GSM9829343 WT_D0_rep3 WT_D0
GSM9829344 WT_D0_rep4 WT_D0
GSM9829345 HET_D0_rep1 HET_D0
GSM9829346 HET_D0_rep2 HET_D0
GSM9829347 HET_D0_rep3 HET_D0
GSM9829348 HET_D0_rep4 HET_D0
GSM9829349 KO_D0_rep1 KO_D0
GSM9829350 KO_D0_rep2 KO_D0
GSM9829351 KO_D0_rep3 KO_D0
GSM9829352 KO_D0_rep4 KO_D0
GSM9829353 WT_D3_rep1 WT_D3
GSM9829354 WT_D3_rep2 WT_D3
GSM9829355 WT_D3_rep3 WT_D3
GSM9829356 WT_D3_rep4 WT_D3
GSM9829357 HET_D3_rep1 HET_D3
GSM9829358 HET_D3_rep2 HET_D3
GSM9829359 HET_D3_rep3 HET_D3
GSM9829360 HET_D3_rep4 HET_D3
GSM9829361 KO_D3_rep1 KO_D3
GSM9829362 KO_D3_rep2 KO_D3
GSM9829363 KO_D3_rep3 KO_D3
GSM9829364 KO_D3_rep4 KO_D3
GSM9829365 WT_D7_rep1 WT_D7
GSM9829366 WT_D7_rep2 WT_D7
GSM9829367 WT_D7_rep3 WT_D7
GSM9829368 WT_D7_rep4 WT_D7
GSM9829369 HET_D7_rep1 HET_D7
GSM9829370 HET_D7_rep2 HET_D7
GSM9829371 HET_D7_rep3 HET_D7
GSM9829372 HET_D7_rep4 HET_D7
GSM9829373 KO_D7_rep1 KO_D7
GSM9829374 KO_D7_rep2 KO_D7
GSM9829375 KO_D7_rep3 KO_D7
GSM9829376 KO_D7_rep4 KO_D7

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