GEO series

A human-specific microRNA controls the timing of excitatory synaptogenesis (miRNA mimics)

GSE310579 Homo sapiens (human) RNA-seq (gene expression) 9 samples Submitted 2026/06/22 Platform GPL24676

At a glance

RNA-seq (gene expression) · human · 9 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: 9 samples: 9 samples, each with a distinct title — no replicated groupsGroups 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)

Neural circuit development in the human cortex is considerably prolonged in comparison to non-human primates, a trait that contributes to the remarkable cognitive capacity of modern humans. Here, we explore the regulatory role of non-coding RNAs, which dramatically expanded during brain evolution, in synapse development of human-induced pluripotent stem-cell derived neurons.

Read the full summary ↓

We found that inhibition of a human-specific microRNA, miR-1229-3p, alters the trajectory of human neuronal maturation and enhances excitatory synaptic transmission. Transcriptome analysis following miR-1229 knockdown revealed a downregulation of mitochondrial DNA (mtDNA) encoded genes. We further show that miR-1229 regulates mitochondrial morphology, mtDNA abundance as well as mitophagy, and that stimulation of mitochondrial metabolism rescues decreased calcium buffering in miR-1229-3p depleted neurons. Accordingly, miR-1229 directly targets an entire network of genes involved in mitochondrial function and ER-associated protein homeostasis. Our findings reveal an important function of human-specific miR-1229-3p in developmental timing of human synaptogenesis and generally implicate non-coding RNAs in the control of human connectivity and cognition.

This dataset

Open GSE310579 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 GSE310579_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 PRJNA1366524 and SRA study SRP646963. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Study design

9 samples, each with a distinct title — no replicated groups

Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.

How we read this: Read from 9 sample titles: 9 distinct titles with little repetition. 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

GSM9304006 N1_Ctrl
GSM9304007 N1_MiR_10nM
GSM9304008 N1_MiR_20nM
GSM9304009 N2_Ctrl
GSM9304010 N2_MiR_10nM
GSM9304011 N2_MiR_20nM
GSM9304012 N3_Ctrl
GSM9304013 N3_MiR_10nM
GSM9304014 N3_MiR_20nM

Datasets on a similar topic

GSE244440 A human-specific microRNA controls the timing of excitatory synaptogenesis (time course ribozero) 21 samples shares human-specific, synaptogenesis, excitatory, microrna, controls, timing
GSE244441 A human-specific microRNA controls the timing of excitatory synaptogenesis (pLNA dataset) 19 samples shares human-specific, synaptogenesis, excitatory, microrna, controls, timing
GSE244444 A human-specific microRNA controls the timing of excitatory synaptogenesis 70 samples shares human-specific, synaptogenesis, excitatory, microrna, controls, timing
GSE243883 CRISPR pooled screen and QuantSeq 3' mRNA sequencing to identify microRNAs (miRNAs) important for Breast Cancer 3D growth [RNA-seq] 24 samples shares microrna, mirna
GSE260873 Excitatory Neurons Derived from Human-Induced Pluripotent Stem Cells Show Transcriptomic Differences in Alzheimer’s Patients from Controls 13 samples shares excitatory, controls
GSE39833 microRNA profiles of serum exosomes in healthy controls and colorectal cancer patients-1 99 samples shares microrna, controls
GSE349625 MicroRNA profiling of freshly isolated human endothelial cells from participants with type 2 diabetes mellitus and non-diabetic controls 38 samples shares microrna, controls
GSE243884 CRISPR pooled screen and QuantSeq 3' mRNA sequencing to identify microRNAs (miRNAs) important for Breast Cancer 3D growth 30 samples shares microrna, mirna

Search all human RNA-seq datasets in GEO →

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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.