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Crnic Institute - Trisomy 21 Model Atlas: PolyA RNA-seq from adult mouse liver tissue

GSE272570 Mus musculus (mouse) RNA-seq (gene expression) 18 samples Submitted 2024/07/18 Platform GPL24247
At a glance

RNA-seq (gene expression) · mouse · 18 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
18 samples: 6 × Wild-type; liver; sample vs 6 × Interferon receptor dosage-normalized (Dp16^2xIFNRs); liver; sample vs 6 × Dp16; liver; sampleGroups 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
Multimodal analysis of dysregulated heme metabolism, hypoxic signaling, and stress erythropoiesis in Down syndromeCell reports · 2024
Summary (written by the submitters)
Analysis of steady-state mRNA levels in adult mouse liver tissue at 17-18 weeks from wild-type C57BL/6J, Dp16, and interferon receptor dosage-normalized Dp16^2xIFNRs mice.
Published in
Multimodal analysis of dysregulated heme metabolism, hypoxic signaling, and stress erythropoiesis in Down syndrome
Donovan MG, Rachubinski AL, Smith KP et al. · Cell reports 2024 · PMID 39120971 · doi:10.1016/j.celrep.2024.114599
This dataset
Open GSE272570 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 GSE272570_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 PRJNA1137359 and SRA study SRP520814. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39120971) ↗
Study design
6 × Wild-type; liver; sample vs 6 × Interferon receptor dosage-normalized (Dp16^2xIFNRs); liver; sample vs 6 × Dp16; liver; sample

Supports a between-group comparison across 18 samples.

How we read this: 3 replicated groups read from 18 sample titles; they account for 18 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 →

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