GEO series
Altered extracellular matrix structure and elevated stiffness in a brain organoid model for disease
GSE228926
Homo sapiens (human)
Non-coding RNA profiling
31 samples
Submitted 2025/01/25
Platform GPL24676
At a glance
Non-coding RNA profiling · human · 31 samples
- What it is
- Non-coding RNA profilingLevels of RNAs that do not code for proteins, such as miRNA or lncRNA.
- Organism
- Homo sapiens (human)
- Samples
- 31 samples: 8 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.
- Paper
- Altered extracellular matrix structure and elevated stiffness in a brain organoid model for diseaseNature communications · 2025
Summary (written by the submitters)
Mutations in Lissencephaly 1 (LIS1) result in various human brain developmental diseases, such as changes in brain structure, lissencephaly, and epilepsy. RNA-sequencing data from on-chip organoids derived from human embryonic stem cells (hESCs) revealed significant changes in the expression of extracellular matrix (ECM) – related genes in LIS1+/- samples.
Read the full summary ↓
This project examined the biomechanical properties of LIS1+/- mutated and healthy hESCs-derived cortical organoids. A rheological test using the pipette aspiration technique revealed that LIS1+/- cortical organoids are stiffer than control organoids. The increased stiffness of the LIS1+/- cortices was proportional to an increased expression of the nuclear mechano-sensing protein, Lamin A, highlighting the adverse cellular and nuclear changes underlying the stiffening of LIS1+/- organoids. To delineate the ECM composition associated with the stiffening effect in LIS1+/-, healthy and mutated hippocampal and cortical organoids were examined at the protein, mRNA, and miRNA levels. Whole RNA sequencing showed altered expression of multiple collagen-related pathways, including the 'collagens containing ECM' and the 'Collagen trimer' pathways. Differential mRNA expression has inversely correlated with the expression of their targeting miRNAs in the LIS1+/- organoids. This inverse miRNA-mRNA expression was most pronounced in genes associated with the ECM-receptor signalling pathway. At the protein level, the mutated hippocampal organoids showed unilateral, substantial increased expression of collagens and proteins involved in collagen synthesis, modification, and remodelling. Following a collagenolytic treatment with the catalytic domain of the MMP9 enzyme, the stiffness levels in the LIS1+/- organoids were reduced to control values. Overall, this work provides new information about the role of LIS1 in controlling collagen expression and the abnormal mechanical properties associated with mutation to the LIS1 gene in the development of the human cortex and hippocampus.
Published in
Karlinski Zur M, Bhattacharya B, Solomonov I et al.
· Nature communications 2025
· PMID 40312467
· doi:10.1038/s41467-025-59252-w
This dataset
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.
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 GSE228926_RAW.tar (it can run to tens of gigabytes).
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.
Also filed as BioProject PRJNA952199 and SRA study SRP430842. Searching any of these in the dataset finder brings you back here.
Study design
8 conditions, mostly with about 4 replicates each
RNA-seq - Wild type organoid day 105, repeat # ×4
RNA-seq - LIS1+/- organoid day 105, repeat # ×4
small RNA-seq - Wild type organoid day 105, r… ×4
small RNA-seq - LIS1+/- organoid day 105, rep… ×4
RNA-seq - Wild type Cntrl organoid day 18, re… ×4
RNA-seq - LIS1+/- Cntrl organoid day 18, repe… ×4
RNA-seq - LIS1+/- MMP9 Treated organoid day 1… ×4
RNA-seq - Wild type MMP9 Treated organoid day… ×3
Supports a case/control comparison: 4 samples read as cases, 12 as controls.
How we read this: 8 replicated groups read from 31 sample titles; they account for 31 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
- GSM7142930 RNA-seq - Wild type organoid day 105, repeat #1 RNA-seq - Wild type org…
- GSM7142931 RNA-seq - Wild type organoid day 105, repeat #2 RNA-seq - Wild type org…
- GSM7142932 RNA-seq - Wild type organoid day 105, repeat #3 RNA-seq - Wild type org…
- GSM7142933 RNA-seq - Wild type organoid day 105, repeat #4 RNA-seq - Wild type org…
- GSM7142934 RNA-seq - LIS1+/- organoid day 105, repeat #1 RNA-seq - LIS1+/- organ…
- GSM7142935 RNA-seq - LIS1+/- organoid day 105, repeat #2 RNA-seq - LIS1+/- organ…
- GSM7142936 RNA-seq - LIS1+/- organoid day 105, repeat #3 RNA-seq - LIS1+/- organ…
- GSM7142937 RNA-seq - LIS1+/- organoid day 105, repeat #4 RNA-seq - LIS1+/- organ…
- GSM7142938 small RNA-seq - Wild type organoid day 105, repeat #1 small RNA-seq - Wild ty…
- GSM7142939 small RNA-seq - Wild type organoid day 105, repeat #2 small RNA-seq - Wild ty…
- GSM7142940 small RNA-seq - Wild type organoid day 105, repeat #3 small RNA-seq - Wild ty…
- GSM7142941 small RNA-seq - Wild type organoid day 105, repeat #4 small RNA-seq - Wild ty…
- GSM7142942 small RNA-seq - LIS1+/- organoid day 105, repeat #1 small RNA-seq - LIS1+/-…
- GSM7142943 small RNA-seq - LIS1+/- organoid day 105, repeat #2 small RNA-seq - LIS1+/-…
- GSM7142944 small RNA-seq - LIS1+/- organoid day 105, repeat #3 small RNA-seq - LIS1+/-…
- GSM7142945 small RNA-seq - LIS1+/- organoid day 105, repeat #4 small RNA-seq - LIS1+/-…
- GSM7142946 RNA-seq - Wild type Cntrl organoid day 18, repeat #1 RNA-seq - Wild type Cnt…
- GSM7142947 RNA-seq - Wild type Cntrl organoid day 18, repeat #2 RNA-seq - Wild type Cnt…
- GSM7142948 RNA-seq - Wild type Cntrl organoid day 18, repeat #3 RNA-seq - Wild type Cnt…
- GSM7142949 RNA-seq - Wild type Cntrl organoid day 18, repeat #4 RNA-seq - Wild type Cnt…
- GSM7142950 RNA-seq - LIS1+/- Cntrl organoid day 18, repeat #1 RNA-seq - LIS1+/- Cntrl…
- GSM7142951 RNA-seq - LIS1+/- Cntrl organoid day 18, repeat #2 RNA-seq - LIS1+/- Cntrl…
- GSM7142952 RNA-seq - LIS1+/- Cntrl organoid day 18, repeat #3 RNA-seq - LIS1+/- Cntrl…
- GSM7142953 RNA-seq - LIS1+/- Cntrl organoid day 18, repeat #4 RNA-seq - LIS1+/- Cntrl…
- GSM7142954 RNA-seq - Wild type MMP9 Treated organoid day 18, repeat #1 RNA-seq - Wild type MMP…
- GSM7142955 RNA-seq - Wild type MMP9 Treated organoid day 18, repeat #2 RNA-seq - Wild type MMP…
- GSM7142956 RNA-seq - Wild type MMP9 Treated organoid day 18, repeat #3 RNA-seq - Wild type MMP…
- GSM7142957 RNA-seq - LIS1+/- MMP9 Treated organoid day 18, repeat #1 RNA-seq - LIS1+/- MMP9 …
- GSM7142958 RNA-seq - LIS1+/- MMP9 Treated organoid day 18, repeat #2 RNA-seq - LIS1+/- MMP9 …
- GSM7142959 RNA-seq - LIS1+/- MMP9 Treated organoid day 18, repeat #3 RNA-seq - LIS1+/- MMP9 …
- GSM7142960 RNA-seq - LIS1+/- MMP9 Treated organoid day 18, repeat #4 RNA-seq - LIS1+/- MMP9 …
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Share this dataset
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.