GEO series

3M-Brazzein, a Natural Sugar Substitute, can Suppress Metabolic Disorders, NAFLD, and Depression-like Behaviors in Diabetic Mice

GSE261723 Mus musculus (mouse) RNA-seq (gene expression) 24 samples Submitted 2024/03/18 Platform GPL24247

At a glance

RNA-seq (gene expression) · mouse · 24 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: 24 samples: 12 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.

Summary (written by the submitters)

The increasing consumption of sugar-sweetened beverages (SSBs) in modern society has enhanced the epidemic of obesity, metabolic disorders, and mental illnesses. Therefore, the current study investigated the potential of 3M-Brazzein as a promising natural sugar substitute. 4-weeks-old leptin receptor knockout mice (db/db) were supplied with water, 10% sucrose solution, or a 3M-Brazzein solution respectively for 16 weeks.

Read the full summary ↓

Chronic consumption of 3M-Brazzein did not cause any degeneration of adipogenesis, insulin resistance, hepatic lipogenesis, and depression-like behaviors. However, 10% sucrose consumed mice exhibited completely different outcomes. Furthermore, the mRNA expression levels of GLUT2, SREBF-1, and PPARγ in liver were significantly increased in knockout mice supplied with the 10% sucrose solution, thereby the excessive sucrose consumption induced severe obesity, impairment of glucose homeostasis, non-alcoholic fatty liver disease (NAFLD), and major depressive disorder in them. Consequently, the present study demonstrated the positive effects of 3M-Brazzein on various health problems prevalent in the modern world, and suggests some genetic clues related to the pathogenesis of NAFLD and major depressive disorder.

This dataset

Open GSE261723 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 GSE261723_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 PRJNA1088492 and SRA study SRP495502. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Study design

12 conditions, mostly in duplicate

Brain, brazzein, db/+, ×2 Brain, sucrose, db/+, ×2 Brain, water, db/+, ×2 Brain, brazzein, db/db, ×2 Brain, sucrose, db/db, ×2 Brain, water, db/db, ×2 Liver, brazzein, db/+, ×2 Liver, sucrose, db/+, ×2 +4 more

Supports a between-group comparison across 24 samples.

How we read this: 12 replicated groups read from 24 sample titles; they account for 24 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

GSM8149633 Brain, brazzein, db/+, rep1 Brain, brazzein, db/+,
GSM8149634 Brain, brazzein, db/+, rep2 Brain, brazzein, db/+,
GSM8149635 Brain, sucrose, db/+, rep1 Brain, sucrose, db/+,
GSM8149636 Brain, sucrose, db/+, rep2 Brain, sucrose, db/+,
GSM8149637 Brain, water, db/+, rep1 Brain, water, db/+,
GSM8149638 Brain, water, db/+, rep2 Brain, water, db/+,
GSM8149639 Brain, brazzein, db/db, rep1 Brain, brazzein, db/db,
GSM8149640 Brain, brazzein, db/db, rep2 Brain, brazzein, db/db,
GSM8149641 Brain, sucrose, db/db, rep1 Brain, sucrose, db/db,
GSM8149642 Brain, sucrose, db/db, rep2 Brain, sucrose, db/db,
GSM8149643 Brain, water, db/db, rep1 Brain, water, db/db,
GSM8149644 Brain, water, db/db, rep2 Brain, water, db/db,
GSM8149645 Liver, brazzein, db/+, rep1 Liver, brazzein, db/+,
GSM8149646 Liver, brazzein, db/+, rep2 Liver, brazzein, db/+,
GSM8149647 Liver, sucrose, db/+, rep1 Liver, sucrose, db/+,
GSM8149648 Liver, sucrose, db/+, rep2 Liver, sucrose, db/+,
GSM8149649 Liver, water, db/+, rep1 Liver, water, db/+,
GSM8149650 Liver, water, db/+, rep2 Liver, water, db/+,
GSM8149651 Liver, brazzein, db/db, rep1 Liver, brazzein, db/db,
GSM8149652 Liver, brazzein, db/db, rep2 Liver, brazzein, db/db,
GSM8149653 Liver, sucrose, db/db, rep1 Liver, sucrose, db/db,
GSM8149654 Liver, sucrose, db/db, rep2 Liver, sucrose, db/db,
GSM8149655 Liver, water, db/db, rep1 Liver, water, db/db,
GSM8149656 Liver, water, db/db, rep2 Liver, water, db/db,

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