← BioTransfer GEO Dataset Finder
GEO series

Loss of Inpp5d has disease-relevant and sex-specific effects on glial transcriptomes

GSE254999 Mus musculus (mouse) Single-cell RNA-seq 12 samples Submitted 2024/06/26 Platform GPL24247
At a glance

Single-cell RNA-seq · mouse · 12 samples

What it is
Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart. Read from the summary: GEO's own type field only says 'expression profiling by sequencing', so confirm it in the paper.
Organism
Mus musculus (mouse)
Samples
12 samples: 6 conditions, mostly in duplicateGroups 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
Loss of Inpp5d has disease-relevant and sex-specific effects on glial transcriptomesAlzheimer's & dementia : the journal of the Alzheimer's Association · 2024
Summary (written by the submitters)
INTRODUCTION: INPP5D is genetically associated with Alzheimer’s disease risk. Loss of Inpp5d alters amyloid pathology in models of amyloidosis. Inpp5d is predominantly expressed in microglia but its function in brain is poorly understood. METHODS: We performed single-cell RNA-sequencing to study the effect of Inpp5d loss on wild-type mouse brain transcriptomes.
Read the full summary ↓
RESULTS: Loss of Inpp5d has sex-specific effects on the brain transcriptome. Affected genes are enriched for multiple neurodegeneration terms. Network analyses reveal a gene co-expression module centered around Inpp5d in female mice. Inpp5d loss alters PTN, PSAP, and VEGFA signaling probability between cell types. DISCUSSION: Our data suggest Inpp5d’s normal function is entangled with mechanisms involved in neurodegeneration. We report the effect of Inpp5d loss without pathology and show that this has dramatic effects on gene expression. Our study provides a critical reference for researchers of neurodegeneration, allowing separation of disease-specific changes mediated by Inpp5d in disease from baseline effects of Inpp5d loss.
Published in
Loss of Inpp5d has disease-relevant and sex-specific effects on glial transcriptomes
Dabin LC, Kersey H, Kim B et al. · Alzheimer's & dementia : the journal of the Alzheimer's Association 2024 · PMID 38923164 · doi:10.1002/alz.13901
This dataset
Open GSE254999 in finder → Find more mouse 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 GSE254999_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: Single-cell studies usually ship their counts as 10x files (matrix.mtx, barcodes.tsv, features.tsv), an .h5 file, or an .rds / .h5ad object that Seurat or Scanpy can open. Look for those among the supplementary files.

Also filed as BioProject PRJNA1072999 and SRA study SRP487940. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 38923164) ↗
Study design
6 conditions, mostly in duplicate
Brain, homozygous knockout female ×2 Brain, homozygous knockout male ×2 Brain, wildtype female ×2 Brain, heterozygous knockout male ×2 Brain, heterozygous knockout female ×2 Brain, wildtype male ×2

Supports a case/control comparison: 8 samples read as cases, 4 as controls.

How we read this: 6 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
Datasets on a similar topic

Search all mouse RNA-seq datasets in GEO →

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.