← BioTransfer GEO Dataset Finder
GEO series

mRNA seq of MOSAICS based Irs1 KO, Srebf1 KO, Tbx3 KO, Bcl6 KO, Smyd2 KO and control (sgGFP and sgLacZ) livers

GSE212916 Mus musculus (mouse) RNA-seq (gene expression) 34 samples Submitted 2024/09/01 Platform GPL19057
At a glance

RNA-seq (gene expression) · mouse · 34 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
34 samples: 7 conditions, mostly with about 5 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.
Summary (written by the submitters)
To investigate expression changes of the KO vs. control livers under 3 months of Western Diet. We then performed mRNA seq analysis on MOSAICS based single-gene whole-liver KO samples and control samples
This dataset
Open GSE212916 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 GSE212916_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 PRJNA878458 and SRA study SRP396237. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
7 conditions, mostly with about 5 replicates each
Tbx3 KO liver # ×7 Smyd2 KO liver # ×6 Bcl6 KO liver # ×5 Irs1 KO liver # ×5 Srebf1 KO liver # ×5 sgGFP control liver # ×4 sgLacZ control liver # ×2

Supports a between-group comparison across 34 samples.

How we read this: 7 replicated groups read from 34 sample titles; they account for 34 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.