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Alzheimer’s disease-induced phagocytic microglia express a specific profile of coding and non-coding RNAs

GSE229419 Mus musculus (mouse) Non-coding RNA profiling 63 samples Submitted 2024/03/20 Platform GPL21493Platform GPL19057
At a glance

Non-coding RNA profiling · mouse · 63 samples

What it is
Non-coding RNA profilingLevels of RNAs that do not code for proteins, such as miRNA or lncRNA.
Organism
Mus musculus (mouse)
Samples
63 samples: 11 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
Alzheimer's disease-induced phagocytic microglia express a specific profile of coding and non-coding RNAsAlzheimer's & dementia : the journal of the Alzheimer's Association · 2024
SuperSeries — this record groups several sub-series.
Summary (written by the submitters)
This SuperSeries is composed of the SubSeries listed below.
Published in
Alzheimer's disease-induced phagocytic microglia express a specific profile of coding and non-coding RNAs
Scoyni F, Giudice L, Väänänen MA et al. · Alzheimer's & dementia : the journal of the Alzheimer's Association 2024 · PMID 37828821 · doi:10.1002/alz.13502
This dataset
Open GSE229419 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 GSE229419_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 ↗

Also filed as BioProject PRJNA954390 and SRA study SRP432023. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 37828821) ↗
Study design
11 conditions, mostly with about 4 replicates each
WT microglia (Me-X04 neg) ×12 TG microglia (Me-X04 neg) ×10 TG microglia (Me-X04 pos) ×9 BV2 vehicle neg ctrl (scramble) ×4 BV2 LPS neg ctrl (scramble) ×4 BV2 vehicle miR-7a ×4 BV2 LPS miR-7a ×4 BV2 vehicle miR-29a ×4 +3 more

Supports a between-group comparison across 63 samples.

How we read this: 11 replicated groups read from 63 sample titles; they account for 63 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

+ 23 more — browse all 63 samples with per-sample file links →

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.