GSE273093
GSE GEOZfp697 is an RNA-binding protein that regulates skeletal muscle inflammation and remodeling (Zfp697 transduced primary mouse myotubes RNA-Seq)
Organism:
Mus musculus
Platform:
GPL17021
Samples:
6
Experiment Types:
Expression profiling by high throughput sequencing
Submitted:
Jul 25 2024
Last Updated:
Jan 21 2026
Status:
Public on Jul 30 2024
Contact:
Igor,,Cervenka (Karolinska Institutet)
Relations
BioProject: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA1140162
Summary
Muscle atrophy is a morbidity and mortality risk factor that happens with disuse, chronic disease, and ageing. Recovery from atrophy involves changes in protein synthesis and different cell types such as muscle fibers, and satellite and immune cells. Here we show that the previously uncharacterized gene and protein Zfp697 is a damage-induced regulator of muscle regeneration. Zfp697/ZNF697 expression is transiently elevated during recovery from muscle atrophy or injury in mice and humans. Sustained Zfp697 expression in mouse muscle leads to a gene expression signature of chemokine secretion, immune cell recruitment, and extracellular matrix remodeling. Myofiber-specific Zfp697 ablation hinders the inflammatory and regenerative response to muscle injury, compromising functional recovery. We uncover Zfp697 as an essential mediator of the interferon gamma response in muscle cells that functions primarily as an ncRNA-binding protein, most notably the pro-regenerative miR-206. This work identifies Zfp697 as an integrator of cell-cell communication necessary for tissue regeneration.
Overall Design
Comparative gene expression profiling analysis of RNA-seq data from differentiated primary mouse myotubes infected with adenovirus endoding either Zfp697 gene or GFP as a control. Experiment contains three replicates for each condition
Analysis (3 steps)
View Data Processing
Processing steps for GSE273093
- Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCm38 whole genome using STAR 2.7.3a with extra arguments --outFilterMultimapNmax 50 --outFilterMultimapScoreRange 3 --outFilterScoreMinOverLread 0.7 --outFilterMatchNminOverLread 0.7 --outFilterMismatchNmax 10 --alignIntronMax 500000 --alignMatesGapMax 1000000 --sjdbScore 2
- Reads aligning to gene exons (Mus_musculus.GRCm38.102.gtf) were counted using featureCounts v2.0.3 program from Subread package, summarized at gene level with extra parameters -s 0
- Differential gene expression at FDR level 0.05 was obtained using DESeq2 R package, genes with total raw counts less then 1 across all samples were excluded from analysis
Supplementary Files (2)
GEO Samples (6)
Dataset Citations (1)
Zfp697 is an RNA-binding protein that regulates skeletal muscle inflammation and remodeling.
PMID 39141348
· 2024
· Proceedings of the National Academy of Sciences of the United States of America
Jorge C Correia, Paulo R Jannig, Maya L Gosztyla, Igor Cervenka, Serge Ducommun, Stine M Præstholm, José M Dias, Kyle D Dumont, Zhengye Liu, Qishan Liang, Daniel Edsgärd, Olof Emanuelsson, Paul Gregorevic, Håkan Westerblad, Tomas Venckunas, Marius Brazaitis, Sigitas Kamandulis, Johanna T Lanner, Ana I Teixeira, Gene W Yeo, Jorge L Ruas
SRA Experiments (6) and Runs (6)
Total: 5404 MBGSM8421732: Myotubes, GFP adenovirus infected, rep1; Mus musculus; RNA-Seq
Sample: SRS22124900
BioProject: PRJNA1140162
BioSample: SAMN42814327
Platform: ILLUMINA
Instrument: Illumina HiSeq 2500
Organism: Mus musculus
Sample attributes
source_name: mouse primary satellite cells
strain: C57BL/6
cell line: mouse primary satellite cells
cell type: myotubes
genotype: wild-type
treatment: Adenovirus infection
condition: Ad_GFP
geo_loc_name: missing
collection_date: missing
Original files (1)
mouse primary satellite cells
Runs (1)
| Run | Spots | Bases | Size (MB) | Files | Link |
|---|---|---|---|---|---|
| SRR29988489 | 44435117 | 2266190967 | 890.05 | GFP_1.fastq.gz, SRR29988489, SRR29988489.lite | SRA |
GSM8421733: Myotubes, GFP adenovirus infected, rep2; Mus musculus; RNA-Seq
Sample: SRS22124902
BioProject: PRJNA1140162
BioSample: SAMN42814326
Platform: ILLUMINA
Instrument: Illumina HiSeq 2500
Organism: Mus musculus
Sample attributes
source_name: mouse primary satellite cells
strain: C57BL/6
cell line: mouse primary satellite cells
cell type: myotubes
genotype: wild-type
treatment: Adenovirus infection
condition: Ad_GFP
geo_loc_name: missing
collection_date: missing
Original files (1)
mouse primary satellite cells
Runs (1)
| Run | Spots | Bases | Size (MB) | Files | Link |
|---|---|---|---|---|---|
| SRR29988488 | 44482199 | 2268592149 | 887.88 | GFP_2.fastq.gz, SRR29988488, SRR29988488.lite | SRA |
GSM8421734: Myotubes, GFP adenovirus infected, rep3; Mus musculus; RNA-Seq
Sample: SRS22124909
BioProject: PRJNA1140162
BioSample: SAMN42814325
Platform: ILLUMINA
Instrument: Illumina HiSeq 2500
Organism: Mus musculus
Sample attributes
source_name: mouse primary satellite cells
strain: C57BL/6
cell line: mouse primary satellite cells
cell type: myotubes
genotype: wild-type
treatment: Adenovirus infection
condition: Ad_GFP
geo_loc_name: missing
collection_date: missing
Original files (1)
mouse primary satellite cells
Runs (1)
| Run | Spots | Bases | Size (MB) | Files | Link |
|---|---|---|---|---|---|
| SRR29988487 | 53390536 | 2722917336 | 1059.5 | GFP_3.fastq.gz, SRR29988487, SRR29988487.lite | SRA |
GSM8421735: Myotubes, Zfp697 adenovirus infected, rep1; Mus musculus; RNA-Seq
Sample: SRS22124904
BioProject: PRJNA1140162
BioSample: SAMN42814324
Platform: ILLUMINA
Instrument: Illumina HiSeq 2500
Organism: Mus musculus
Sample attributes
source_name: mouse primary satellite cells
strain: C57BL/6
cell line: mouse primary satellite cells
cell type: myotubes
genotype: wild-type
treatment: Adenovirus infection
condition: Ad_Zfp697
geo_loc_name: missing
collection_date: missing
Original files (1)
mouse primary satellite cells
Runs (1)
| Run | Spots | Bases | Size (MB) | Files | Link |
|---|---|---|---|---|---|
| SRR29988486 | 41985961 | 2141284011 | 820.08 | Zfp697_1.fastq.gz, SRR29988486, SRR29988486.lite | SRA |
GSM8421736: Myotubes, Zfp697 adenovirus infected, rep2; Mus musculus; RNA-Seq
Sample: SRS22124912
BioProject: PRJNA1140162
BioSample: SAMN42814323
Platform: ILLUMINA
Instrument: Illumina HiSeq 2500
Organism: Mus musculus
Sample attributes
source_name: mouse primary satellite cells
strain: C57BL/6
cell line: mouse primary satellite cells
cell type: myotubes
genotype: wild-type
treatment: Adenovirus infection
condition: Ad_Zfp697
geo_loc_name: missing
collection_date: missing
Original files (1)
mouse primary satellite cells
Runs (1)
| Run | Spots | Bases | Size (MB) | Files | Link |
|---|---|---|---|---|---|
| SRR29988485 | 30097501 | 1534972551 | 832.83 | Zfp697_2.fastq.gz, SRR29988485, SRR29988485.lite | SRA |
GSM8421737: Myotubes, Zfp697 adenovirus infected, rep3; Mus musculus; RNA-Seq
Sample: SRS22124903
BioProject: PRJNA1140162
BioSample: SAMN42814322
Platform: ILLUMINA
Instrument: Illumina HiSeq 2500
Organism: Mus musculus
Sample attributes
source_name: mouse primary satellite cells
strain: C57BL/6
cell line: mouse primary satellite cells
cell type: myotubes
genotype: wild-type
treatment: Adenovirus infection
condition: Ad_Zfp697
geo_loc_name: missing
collection_date: missing
Original files (1)
mouse primary satellite cells
Runs (1)
| Run | Spots | Bases | Size (MB) | Files | Link |
|---|---|---|---|---|---|
| SRR29988484 | 46702853 | 2381845503 | 913.78 | Zfp697_3.fastq.gz, SRR29988484, SRR29988484.lite | SRA |
Linked Publications (2)
Zfp697 is an RNA-binding protein that regulates skeletal muscle inflammation and remodeling.
Proceedings of the National Academy of Sciences of the United States of America · 2024
Zfp697 is an RNA-binding protein that regulates skeletal muscle inflammation and remodeling.
Proceedings of the National Academy of Sciences of the United States of America · 2024
Data Files (6)
| Accession | File Name | Stored Type | Output Type | Mapping Assembly | Size | Download | |
|---|---|---|---|---|---|---|---|
| — | GFP_1.fastq.gz | RNA-Seq | 890.0 MB | link | |||
| — | GFP_2.fastq.gz | RNA-Seq | 887.9 MB | link | |||
| — | GFP_3.fastq.gz | RNA-Seq | 1.0 GB | link | |||
| — | Zfp697_1.fastq.gz | RNA-Seq | 820.1 MB | link | |||
| — | Zfp697_2.fastq.gz | RNA-Seq | 832.8 MB | link | |||
| — | Zfp697_3.fastq.gz | RNA-Seq | 913.8 MB | link |