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Identifying key regulatory networks and predicting targets of orphan box C/D SNORD116 snoRNAs in Prader-Willi Syndrome

GSE232183 Homo sapiens (human) RNA-seq (gene expression) 39 samples Submitted 2024/08/29 Platform GPL24676Platform GPL21697
At a glance

RNA-seq (gene expression) · human · 39 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
39 samples: 7 conditions, mostly with about 6 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
Identifying key underlying regulatory networks and predicting targets of orphan C/D box SNORD116 snoRNAs in Prader-Willi syndromeNucleic acids research · 2024
Summary (written by the submitters)
To identify the targets and functions of SNORD116 snoRNAs, we engineered two different deletions mimicking those seen in Prader-Willi Syndrome (PWS) patients into two distinct human embryonic stem cell lines to control for effects of genetic background. We also introduced an inducible Neurogenin-2 cassette into the safe-harbor AAVS1 locus to enable quick and reproducible differentiation into neurons.
Read the full summary ↓
We verified wild type and deletion genotypes across both genetic background generated comparable neruons at a gene expression level by comparing them to wild type hESCs. We then performed differential gene expression analysis using data obtained from bulk RNA-sequencing to compare the two distinct deletion types to their isogenic wild type pair and each other.
Published in
Identifying key underlying regulatory networks and predicting targets of orphan C/D box SNORD116 snoRNAs in Prader-Willi syndrome
Gilmore RB, Liu Y, Stoddard CE et al. · Nucleic acids research 2024 · PMID 39575480 · doi:10.1093/nar/gkae1129
This dataset
Open GSE232183 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 GSE232183_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 PRJNA971186 and SRA study SRP436909. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39575480) ↗
Study design
7 conditions, mostly with about 6 replicates each
CT2 neurons, wild type (WT) + NGN, biol ×6 CT2 neurons, delSNORD116 (smDEL) + NGN, biol ×6 CT2 neurons, delPWSIC-IPW (lgDEL) + NGN, biol ×6 H9 neurons, wild type (WT) + NGN, biol ×6 H9 neurons, delPWSIC-IPW (lgDEL) + NGN, biol ×6 H9 neurons, delSNORD116 (smDEL) + NGN, biol ×5 H9 ESCs, wild type (WT), biol ×4

Supports a between-group comparison across 39 samples.

How we read this: 7 replicated groups read from 39 sample titles; they account for 39 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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