GEO series

Excitatory cortical neurons from CDKL5 deficiency disorder patient-derived organoids show early hyperexcitability not identified in neurogenin2 induced neurons [RNA-Seq]

GSE319077 Homo sapiens (human) RNA-seq (gene expression) 18 samples Submitted 2026/03/17 Platform GPL24676

At a glance

RNA-seq (gene expression) · human · 18 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: 18 samples: 6 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)

CDKL5 deficiency disorder (CDD) is a rare developmental and epileptic encephalopathy resulting from variants in cyclin-dependent kinase-like 5 (CDKL5) that lead to impaired kinase activity or loss of function. CDD is one of the most common genetic etiologies identified in epilepsy cohorts. To study how CDKL5 variants impact human neuronal activity, gene expression and morphology, CDD patient-derived induced pluripotent stem cells and their isogenic controls were differentiated into excitatory neurons using either an NGN2 induction protocol or a guided cortical organoid differentiation.

Read the full summary ↓

Patient-derived neurons from both differentiation paradigms had decreased phosphorylated EB2, a known molecular target of CDKL5. Induced neurons showed no detectable differences between cases and isogenic controls in network activity using a multielectrode array, or in MAP2+ neurite length, and only two genes were differentially expressed. However, patient-derived neurons from the organoid differentiation showed increased synchrony and weighted mean firing rate on the multielectrode array within the first month of network maturation. CDD patient-derived cortical neurons had lower expression of CDKL5 and HS3ST1, which may change the extracellular matrix around the synapse and contribute to hyperexcitability. Similar to the induced neurons, there were no differences in neurite length across or within patient-control cell lines. Induced neurons have poor cortical specification while the organoid derived neurons expressed cortical markers, suggesting that the changes in neuronal excitability and gene expression are specific to cortical excitatory neurons. Examining molecular mechanisms of early hyperexcitability in cortical neurons is a promising avenue for identification of CDD therapeutics.

This dataset

Open GSE319077 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 GSE319077_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 PRJNA1422059. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Study design

6 conditions, mostly in triplicate

HNDS0022_D ×3 HNDS0022_A ×3 HNDS0083_D ×3 HNDS0083_B ×3 MAN0855_D ×3 MAN0855_A ×3

Supports a between-group comparison across 18 samples.

How we read this: 6 replicated groups read from 18 sample titles; they account for 18 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

GSM9509599 HNDS0022_D_Rep1 HNDS0022_D
GSM9509600 HNDS0022_A_Rep1 HNDS0022_A
GSM9509601 HNDS0022_D_Rep2 HNDS0022_D
GSM9509602 HNDS0022_A_Rep2 HNDS0022_A
GSM9509603 HNDS0022_D_Rep3 HNDS0022_D
GSM9509604 HNDS0022_A_Rep3 HNDS0022_A
GSM9509605 HNDS0083_D_Rep1 HNDS0083_D
GSM9509606 HNDS0083_B_Rep1 HNDS0083_B
GSM9509607 HNDS0083_D_Rep2 HNDS0083_D
GSM9509608 HNDS0083_B_Rep2 HNDS0083_B
GSM9509609 HNDS0083_D_Rep3 HNDS0083_D
GSM9509610 HNDS0083_B_Rep3 HNDS0083_B
GSM9509611 MAN0855_D_Rep1 MAN0855_D
GSM9509612 MAN0855_A_Rep1 MAN0855_A
GSM9509613 MAN0855_D_Rep2 MAN0855_D
GSM9509614 MAN0855_A_Rep2 MAN0855_A
GSM9509615 MAN0855_D_Rep3 MAN0855_D
GSM9509616 MAN0855_A_Rep3 MAN0855_A

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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.