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Effects of selective elimination of senescent cells on RPE/choroid complex in mice with subretinal drusenoid deposits

GSE234641 Mus musculus (mouse) RNA-seq (gene expression) 15 samples Submitted 2024/04/17 Platform GPL24247
At a glance

RNA-seq (gene expression) · mouse · 15 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
Mus musculus (mouse)
Samples
15 samples: 8 × RPE/choroid complex, INK-ATTAC vs 7 × RPE/choroid complex, controlGroups 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
LXR/CD38 activation drives cholesterol-induced macrophage senescence and neurodegeneration via NAD(+) depletionCell reports · 2024
Summary (written by the submitters)
The target deletion of ATP binding cassette subfamily member 1 (ABCA1) and G1 (ABCG1) in myeloid cells leads to subretinal drusenoid deposits in mice (Abca1/g1 -m/-m). We here report the selective elimination of p16-positive cells results in the significant eduction in myeloid markers, pro-inflammatory cytokines and prostaglandin biosynthetic enzymes.
Published in
LXR/CD38 activation drives cholesterol-induced macrophage senescence and neurodegeneration via NAD(+) depletion
Terao R, Lee TJ, Colasanti J et al. · Cell reports 2024 · PMID 38636518 · doi:10.1016/j.celrep.2024.114102
This dataset
Open GSE234641 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 GSE234641_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 PRJNA982173 and SRA study SRP442176. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 38636518) ↗
Study design
8 × RPE/choroid complex, INK-ATTAC vs 7 × RPE/choroid complex, control

Supports a between-group comparison across 15 samples.

How we read this: 2 replicated groups read from 15 sample titles; they account for 15 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

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