← BioTransfer GEO Dataset Finder
GEO series

Effect of knockdown of Zbtb9 on gene expression during adipogenic differentiation of 3T3-L1 preadipocytes

GSE253544 Mus musculus (mouse) RNA-seq (gene expression) 32 samples Submitted 2024/11/14 Platform GPL24247
At a glance

RNA-seq (gene expression) · mouse · 32 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
32 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.
Paper
Cell-state-dependent regulation of PPARγ signaling by the transcription factor ZBTB9 in adipocytesThe Journal of biological chemistry · 2024
Summary (written by the submitters)
Adipocytes play a critical role in metabolic homeostasis. Here we report that Zbtb9 acts as a positive regulator of PPARγ transcriptional activity in 3T3-L1 mature adipocytes, and PPARγ target gene expression was decreased when Zbtb9 deficiency was induced by shRNA-mediated knockdown (KD), establishing Zbtb9 as a newly identified PPARγ cofactor.
Read the full summary ↓
Given the central role of PPARγ in adipogenesis, we also sought to investigate the role of Zbtb9 in adipogenesis in 3T3-L1 cells. Surprisingly, lipid droplet formation was significantly increased in Zbtb9 KD cells compared with the control, as was the expression of adipogenic genes including Pparg, Adipoq, Fabp4, and Cd36. The transcriptome of Zbtb9-KD fibroblasts, prior to the initiation of differentiation showed that the E2F targets pathway was significantly upregulated compared to the control cells. In addition, E2F activity was increased in Zbtb9-KD fibroblasts using luciferase reporter assay. Accordingly, RB phosphorylation was enhanced in Zbtb9-KD cells. Collectively, these results demonstrate that Zbtb9 inhibits adipogenesis as a negative regulator of Pparg expression via altered pRB-E2F1 signaling. Together, our findings revealed complex cell-state dependent roles of Zbtb9 in adipocytes, identifying a new molecule that may be important in the pathogenesis and treatment of obesity and T2D.
Published in
Cell-state-dependent regulation of PPARγ signaling by the transcription factor ZBTB9 in adipocytes
Xu X, Charrier A, Congrove S et al. · The Journal of biological chemistry 2024 · PMID 39542250 · doi:10.1016/j.jbc.2024.107985
This dataset
Open GSE253544 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 GSE253544_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 PRJNA1066263 and SRA study SRP484443. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39542250) ↗
Study design
12 conditions, mostly in duplicate
3T3-L1 cells, shCtrl, Day0, ×4 3T3-L1 cells, shCtrl, Day3, ×4 3T3-L1 cells, shCtrl, Day7, ×4 3T3-L1 cells, shCtrl, Day11, ×4 3T3-L1 cells, shRNA #1, Day0, ×2 3T3-L1 cells, shRNA #2, Day0, ×2 3T3-L1 cells, shRNA #1, Day3, ×2 3T3-L1 cells, shRNA #2, Day3, ×2 +4 more

Supports a between-group comparison across 32 samples.

How we read this: 12 replicated groups read from 32 sample titles; they account for 32 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.