GEO series

A human-specific microRNA controls the timing of excitatory synaptogenesis (pLNA dataset)

GSE244441 Homo sapiens (human) RNA-seq (gene expression) 19 samples Submitted 2025/10/30 Platform GPL24676

At a glance

RNA-seq (gene expression) · human · 19 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: 19 samples: 16 distinct titles, 3 of them repeatedGroups 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 GSE244441 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 GSE244441_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 PRJNA1023177 and SRA study SRP464150. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Study design

16 distinct titles, 3 of them repeated

p3_pLNA ×2 p4_pLNA ×2 p2_pLNA ×2

How we read this: Read from 19 sample titles: 16 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

GSM7816191 p4_Empty
GSM7816192 p1_pLNA-3943
GSM7816193 p3_pLNA-Ctrl
GSM7816194 p3_pLNA-3943
GSM7816195 p2_pLNA-181c
GSM7816196 p4_pLNA-1229
GSM7816197 p2_Empty
GSM7816198 p1_pLNA-Ctrl
GSM7816199 p2_pLNA-Ctrl
GSM7816200 p3_pLNA-1229
GSM7816201 p2_pLNA-3943
GSM7816202 p3_Empty
GSM7816203 p4_pLNA-3943
GSM7816204 p3_pLNA-181c
GSM7816205 p2_pLNA-1229
GSM7816206 p4_pLNA-Ctrl
GSM7816207 p1_Empty
GSM7816208 p4_pLNA-181c
GSM7816209 p1_pLNA-181c

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
GSE310579 A human-specific microRNA controls the timing of excitatory synaptogenesis (miRNA mimics) 9 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
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
GSE40246 microRNA profiles of serum exosomes in healthy controls and colorectal cancer patients-2 24 samples shares microrna, controls
GSE324961 microRNA-132 attenuates inflammation in induced pluripotent stem-cell derived microglia from Alzheimer’s disease patients 95 samples shares microrna

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.