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Dysregulation of global mRNA splicing in a Huntington’s disease neuronal differentiation cell line model

GSE217469 Homo sapiens (human) RNA-seq (gene expression) 27 samples Submitted 2024/09/17 Platform GPL11154
At a glance

RNA-seq (gene expression) · human · 27 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
27 samples: 9 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.
Paper
Widespread dysregulation of mRNA splicing implicates RNA processing in the development and progression of Huntington's diseaseEBioMedicine · 2023
Summary (written by the submitters)
To study cell type- and HTT CAG length-dependent transcriptional and alternative splicing changes associated with HD, we conducted deep RNA-sequencing analysis on human embryonic stem cells (hESC), NPC and neuron cell lines (ESC and NPC, NEU) expressing wild-type (27/ and 30 CAG repeats), 45 CAG (45Q; representing 45 polyQ mutant HTT protein) and 81 CAG (81Q) repeat expansion HTT gene (n=3).
Read the full summary ↓
The cell lines were derived from an isogenic HTT CAG repeat expansion allelic cell line panel (IsoHD) where hESC H9 cells were genetically modified with monoallelic knockin of expanded CAG tract in exon 1 of HTT representing early onset (45Q) and late onset (81Q) HD, with the 27Q/30Q genotype as healthy control phenotype (Ooi et al., 2019). The sequencing experiment generated 2.9 billion pairs of 150 bp paired-end reads from 27 samples (3 clones, 3 genotypes, 3 cell lines), with 80 to 110 million read pairs per sample. Transcriptome alignment yielded 75 to 100 million uniquely mapped read pairs across all samples.
Published in
Widespread dysregulation of mRNA splicing implicates RNA processing in the development and progression of Huntington's disease
Tano V, Utami KH, Yusof NABM et al. · EBioMedicine 2023 · PMID 37481821 · doi:10.1016/j.ebiom.2023.104720
This dataset
Open GSE217469 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 GSE217469_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 PRJNA899069 and SRA study SRP406691. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 37481821) ↗
Study design
9 conditions, mostly in triplicate
hESC, H9 control, ×3 hESC, 45 CAG repeat HTT, ×3 hESC, 81 CAG repeat HTT, ×3 NPC, H9 control, ×3 NPC, 45 CAG repeat HTT, ×3 NPC, 81 CAG repeat HTT, ×3 Neuron, H9 control, ×3 Neuron, 45 CAG repeat HTT, ×3 +1 more

Supports a between-group comparison across 27 samples.

How we read this: 9 replicated groups read from 27 sample titles; they account for 27 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
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