Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Profiling Mouse Brown and White Adipocytes to Identify Metabolically Relevant small ORFs and Functional Microproteins [Ribo-seq]

ABSTRACT: Profiling Mouse Brown and White Adipocytes to Identify Metabolically Relevant small ORFs and Functional Microproteins [Ribo-seq]

PROVIDER: PRJNA812862 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR18220721.fastq.gz	Fastqsanger.gz
	SRR18220722.fastq.gz	Fastqsanger.gz
	SRR18220723.fastq.gz	Fastqsanger.gz
	SRR18220724.fastq.gz	Fastqsanger.gz
	SRR18220725.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 6

Similar Datasets

Profiling Mouse Brown and White Adipocytes to Identify Metabolically Relevant small ORFs and Functional Microproteins [Ribo-seq]

Project description:The absence of thousands of recently annotated small open reading frame (smORF)-encoded peptides and small proteins (microproteins) from databases has precluded their analysis in metabolism and metabolic disease. Given the outsized importance of small proteins and peptides in metabolism—insulin, leptin, amylin, glucagon, and glucagon-like peptide-1 (GLP-1)—microproteins are a potentially rich source of uncharacterized metabolic regulators. Here, we annotate smORFs in primary differentiated brown, white, and beige mouse adipose cells. Ribosome profiling (Ribo-Seq) detected a total of 3,877 unannotated smORFs. Analysis of RNA-Seq datasets revealed diet-regulated smORF expression in adipose tissues, and validated the adipose translation of the feeding-neuron marker gene Gm8773. Gm8773 encodes the mouse homolog of FAM237B, a neurosecretory protein that stimulates food intake and promotes weight gain in chickens. Testing of recombinant mFAM237B produced similar orexigenic activity in mice further supporting a role for FAM237B a metabolic regulator and part of the brain-adipose axis. Furthermore, we showed that data independent acquisition mass spectrometry (DIA-MS) proteomics can provide a sensitive, flexible, and quantitative platform for identifying microproteins by mass spectrometry. Using this system led to the detection of 58 microproteins from cell culture and an additional 25 from mouse serum. The proteomics data established the anti-inflammatory microprotein AW112010 as a circulating factor, and found that serum levels of a microprotein translated from a FRS2 uORF is elevated in older obese mice. Together, the data highlight the value of this database in examining understudied smORFs and microproteins in metabolic research and identifying additional regulators of metabolism.

2022-12-13 | GSE197909 | GEO

Profiling Mouse Brown and White Adipocytes to Identify Metabolically Relevant small ORFs and Functional Microproteins [RNA-seq]

2022-12-13 | GSE198107 | GEO

Profiling Mouse Brown and White Adipocytes to Identify Metabolically Relevant small ORFs and Functional Microproteins

Project description:Profiling Mouse Brown and White Adipocytes to Identify Metabolically Relevant small ORFs and Functional Microproteins

| PRJNA813623 | ENA

Profiling Mouse Brown and White Adipocytes to Identify Metabolically Relevant small ORFs and Functional Microproteins [RNA-seq]

Project description:Profiling Mouse Brown and White Adipocytes to Identify Metabolically Relevant small ORFs and Functional Microproteins [RNA-seq]

| PRJNA813625 | ENA

Profiling mouse brown and white adipocytes to identify metabolically relevant small ORFs and functional microproteins.

Project description:Microproteins (MPs) are a potentially rich source of uncharacterized metabolic regulators. Here, we use ribosome profiling (Ribo-seq) to curate 3,877 unannotated MP-encoding small ORFs (smORFs) in primary brown, white, and beige mouse adipocytes. Of these, we validated 85 MPs by proteomics, including 33 circulating MPs in mouse plasma. Analyses of MP-encoding mRNAs under different physiological conditions (high-fat diet) revealed that numerous MPs are regulated in adipose tissue in vivo and are co-expressed with established metabolic genes. Furthermore, Ribo-seq provided evidence for the translation of Gm8773, which encodes a secreted MP that is homologous to human and chicken FAM237B. Gm8773 is highly expressed in the arcuate nucleus of the hypothalamus, and intracerebroventricular administration of recombinant mFAM237B showed orexigenic activity in obese mice. Together, these data highlight the value of this adipocyte MP database in identifying MPs with roles in fundamental metabolic and physiological processes such as feeding.

| S-EPMC9889109 | biostudies-literature

Profiling Mouse Brown and White Adipocytes to Identify Metabolically Relevant small ORFs and Functional Microproteins

Project description:This SuperSeries is composed of the SubSeries listed below.

2022-12-13 | GSE198109 | GEO

CRISPR-Cas9 Screening Reveals Microproteins Regulating Adipocyte Proliferation and Lipid Metabolism [Ribo-seq]

Project description:Small open reading frames (smORFs) encode microproteins that play crucial roles in various biological processes, yet their functions in adipocyte biology remain largely unexplored. In a previous study, we identified thousands of smORFs in white and brown adipocytes derived from the stromal vascular fraction (SVF) of mice using ribosome profiling (Ribo-Seq). Here, we expand on this work by identifying additional smORFs related to adipocytes using the in vitro 3T3-L1 preadipocyte model. To systematically investigate the functional relevance of these smORFs, we designed a custom CRISPR/Cas9 guide RNA (sgRNA) library and screened for smORFs influencing adipocyte proliferation and differentiation. Through a dropout screen and fluorescence-assisted cell sorting (FACS) of lipid droplets, we identified dozens of smORFs that regulate either cell proliferation or lipid accumulation. Among these, we validated a novel microprotein as a key regulator of adipocyte differentiation. These findings highlight the potential of CRISPR/Cas9-based screening to uncover functional smORFs and provide a framework for further exploration of microproteins in adipocyte biology and metabolic regulation.

2025-08-27 | GSE297348 | GEO

Improved Super-Resolution Ribosome Profiling Reveals Prevalent Translation of Upstream ORFs and Small ORFs in Arabidopsis

Project description:We used Ribo-seq (Ribosome profiling) combining with RNA-seq to explore the translational landscape of Arabidopsis Col-0 seedling. We generated 6 biological replicates of RNA-seq and Ribo-seq data for Arabidopsis Col-0 seedling. 3 of the replicates were collected after 20 minutes of 0.1% DMSO treatment and the other 3 samples were collected after 60 minutes of DMSO treatmeant. The resulting RNA-seq and Ribo-seq files were used to discover translated up-stream ORFs (uORFs) and analyze the translation efficiency of uORF-containing genes in Arabidopsis.

2023-09-20 | GSE183264 | GEO

CRISPR-Cas9 Screening Reveals Microproteins Regulating Adipocyte Proliferation and Lipid Metabolism [Ribo-seq]

Project description:CRISPR-Cas9 Screening Reveals Microproteins Regulating Adipocyte Proliferation and Lipid Metabolism [Ribo-seq]

| PRJNA1263619 | ENA

Characterization of miP1a/b (microProteins) overexpression plants, including a constans mutant (co-SAIL)

Project description:MicroProteins are short, single domain proteins that act by sequestering larger, multidomain proteins into non-functional complexes. MicroProteins have been identified in plants and animals, where they are mostly involved in the regulation of developmental processes. Here we show that two Arabidopsis thaliana microProteins, miP1a and miP1b, physically interact with CONSTANS (CO) a potent regulator of flowering time. The miP1a/b-type microProteins evolved in dicotyledonous plants and have an additional carboxy-terminal PF(V/L)FL motif. This motif enables miP1a/b microProteins to interact with TOPLESS/TOPLESS-RELATED (TPL/TPR) proteins. Interaction of CO with miP1a/b/TPL causes late flowering due to a failure in the induction of FLOWERING LOCUS T (FT) expression under inductive long day conditions. Both miP1a and miP1b are expressed in vascular tissue, where CO and FT are active. Genetically, miP1a/b act upstream of CO thus our findings unravel a novel layer of flowering time regulation via microProtein-inhibition. RNA-Seq transcriptome analysis of four biological samples were analysed with two technical replicates. Columbia wildtype plants Col-0, constans mutant plants co-SAIL, and two transgenic lines overexpressing a microProtein (miP1a and miP1b) were sequenced.

2016-03-08 | E-GEOD-56811 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data