GEO series

ELMSAN1 Regulates Differentiation and Maturation of Cardiomyocytes Derived from Human Induced Pluripotent Stem Cells

GSE262838 Homo sapiens (human) RNA-seq (gene expression) 12 samples Submitted 2024/07/25 Platform GPL24676

At a glance

RNA-seq (gene expression) · human · 12 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: 12 samples: 3 × KO, Day 0, vs 3 × WT, Day 0, vs 3 × KO, Day 9, vs 3 × WT, Day 9,Groups 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: ELM2-SANT Domain-Containing Scaffolding Protein 1 Regulates Differentiation and Maturation of Cardiomyocytes Derived From Human-Induced Pluripotent Stem CellsJournal of the American Heart Association · 2024

Summary (written by the submitters)

Background ELMSAN1 is a newly identified scaffolding protein of the mitotic deacetylase complex (MiDAC), playing a pivotal role in early embryonic development. Studies on Elmsan1 knockout mice showed that its absence results in embryo lethality and heart malformation. However, the precise function of ELMSAN1 in heart development and formation has remained elusive.

Read the full summary ↓

To gain insights into its potential role in cardiac lineage, we employed human-induced pluripotent stem cells (hiPSCs) to model early cardiogenesis and investigated the function of ELMSAN1. Methods and Results We generated ELMSAN1-deficient hiPSCs through both knockdown and knockout, revealing that ELMSAN1 appears to be unnecessary for hiPSC maintenance. During the process of cardiac differentiation, ELMSAN1 depletion led to a delay in pluripotency deactivation, decreased expression of cardiac-specific markers, and reduced differentiation efficiency. The impaired expression of genes associated with contractile sarcomere structure, calcium handling, and ion channels were also noted in ELMSAN1-deficient cardiomyocytes derived from hiPSCs (hiPSC-CMs). Additionally, through a series of structural and functional assessments, we found that these cells are immature, exhibiting incomplete sarcomere Z-line structure and length, decreased calcium amplitude, increased time to peak value, faster beat rate with a shorter beat period, decreased field potential duration, and prolonged propagation delay. Of note, we found that the cardiac specific role of ELMSAN1 is likely associated with histone H3K27 acetylation level. The transcriptome analysis provided additional insights, indicating maturation reduction with energy metabolism switch and restored cell proliferation in ELMSAN1 knockout cardiomyocytes. Conclusions In this study, we address the significance of the direct involvement of ELMSAN1 in the differentiation and maturation of hiPSC-CMs. We first report the impact of ELMSAN1 on multiple aspects of hiPSC-CM generation, including cardiac differentiation, sarcomere formation, calcium handling, electrophysiological maturation and proliferation.

Published in

ELM2-SANT Domain-Containing Scaffolding Protein 1 Regulates Differentiation and Maturation of Cardiomyocytes Derived From Human-Induced Pluripotent Stem Cells

Lu YA, Sun J, Wang L et al. · Journal of the American Heart Association 2024 · PMID 38904247 · doi:10.1161/JAHA.124.034816

This dataset

Open GSE262838 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 GSE262838_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 PRJNA1093459 and SRA study SRP498683. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 38904247) ↗

Study design

3 × KO, Day 0, vs 3 × WT, Day 0, vs 3 × KO, Day 9, vs 3 × WT, Day 9,

Supports a between-group comparison across 12 samples.

How we read this: 4 replicated groups read from 12 sample titles; they account for 12 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

GSM8180235 KO, Day 0, replicate 1 KO, Day 0,
GSM8180236 KO, Day 0, replicate 2 KO, Day 0,
GSM8180237 KO, Day 0, replicate 3 KO, Day 0,
GSM8180238 WT, Day 0, replicate 1 WT, Day 0,
GSM8180239 WT, Day 0, replicate 2 WT, Day 0,
GSM8180240 WT, Day 0, replicate 3 WT, Day 0,
GSM8180241 KO, Day 9, replicate 1 KO, Day 9,
GSM8180242 KO, Day 9, replicate 2 KO, Day 9,
GSM8180243 KO, Day 9, replicate 3 KO, Day 9,
GSM8180244 WT, Day 9, replicate 1 WT, Day 9,
GSM8180245 WT, Day 9, replicate 2 WT, Day 9,
GSM8180246 WT, Day 9, replicate 3 WT, Day 9,

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