GSE273094
GSE GEOZfp697 is an RNA-binding protein that regulates skeletal muscle inflammation and remodeling (Zfp697 transduced primary mouse myotubes ChIP-Seq)
Organism:
Mus musculus
Platform:
GPL21626
Samples:
7
Experiment Types:
Genome binding/occupancy 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/PRJNA1140161
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
Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for Flag and normal mouse IgG as a control in differentiated mouse myotubes transduced with Flag-Zfp697 adenovirus. Experiment was performed in triplicates.
Analysis (3 steps)
View Data Processing
Processing steps for GSE273094
- Reads were aligned to the GRCm38.p6 version of the mouse genome using STAR and duplicated reads were removed with MarkDuplicates.
- We used MACS3 callpeak for peak calling (q- value < 0.05 and fold change ⥠1.5).
- Bedtools were used to generate coverage tracks.
Supplementary Files (1)
GSE273094_RAW.tar
Download
GEO Samples (7)
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 (7) and Runs (7)
Total: 19464 MBGSM8421738: Myotubes, Ad Flag-Zfp697, Flag ab, rep1; Mus musculus; ChIP-Seq
Sample: SRS22124849
BioProject: PRJNA1140161
BioSample: SAMN42814321
Platform: ILLUMINA
Instrument: NextSeq 550
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 Flag-Zfp697
chip antibody: FLAG (F3165, Sigma)
geo_loc_name: missing
collection_date: missing
Original files (1)
mouse primary satellite cells
Runs (1)
| Run | Spots | Bases | Size (MB) | Files | Link |
|---|---|---|---|---|---|
| SRR29988228 | 30120326 | 3915642380 | 1194.37 | FLAG_1_S4_1.fastq.gz, FLAG_1_S4_2.fastq.gz, SRR29988228, SRR29988228.… | SRA |
GSM8421739: Myotubes, Ad Flag-Zfp697, Flag ab, rep2; Mus musculus; ChIP-Seq
Sample: SRS22124848
BioProject: PRJNA1140161
BioSample: SAMN42814320
Platform: ILLUMINA
Instrument: NextSeq 550
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 Flag-Zfp697
chip antibody: FLAG (F3165, Sigma)
geo_loc_name: missing
collection_date: missing
Original files (1)
mouse primary satellite cells
Runs (1)
| Run | Spots | Bases | Size (MB) | Files | Link |
|---|---|---|---|---|---|
| SRR29988227 | 81308114 | 10570054820 | 3211.75 | FLAG_2_S5_1.fastq.gz, FLAG_2_S5_2.fastq.gz, SRR29988227, SRR29988227.… | SRA |
GSM8421740: Myotubes, Ad Flag-Zfp697, Flag ab, rep3; Mus musculus; ChIP-Seq
Sample: SRS22124847
BioProject: PRJNA1140161
BioSample: SAMN42814319
Platform: ILLUMINA
Instrument: NextSeq 550
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 Flag-Zfp697
chip antibody: FLAG (F3165, Sigma)
geo_loc_name: missing
collection_date: missing
Original files (1)
mouse primary satellite cells
Runs (1)
| Run | Spots | Bases | Size (MB) | Files | Link |
|---|---|---|---|---|---|
| SRR29988226 | 83228442 | 10819697460 | 3293.03 | SRR29988226.lite, SRR29988226, FLAG_3_S6_2.fastq.gz, FLAG_3_S6_1.fast… | SRA |
GSM8421741: Myotubes, Ad Flag-Zfp697, Input; Mus musculus; ChIP-Seq
Sample: SRS22124850
BioProject: PRJNA1140161
BioSample: SAMN42814318
Platform: ILLUMINA
Instrument: NextSeq 550
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 Flag-Zfp697
chip antibody: None
geo_loc_name: missing
collection_date: missing
Original files (1)
mouse primary satellite cells
Runs (1)
| Run | Spots | Bases | Size (MB) | Files | Link |
|---|---|---|---|---|---|
| SRR29988225 | 114410936 | 14873421680 | 4466.09 | Input3_S7_1.fastq.gz, Input3_S7_2.fastq.gz, SRR29988225, SRR29988225.… | SRA |
GSM8421742: Myotubes, Ad Flag-Zfp697, mIgG ab, rep1; Mus musculus; ChIP-Seq
Sample: SRS22124852
BioProject: PRJNA1140161
BioSample: SAMN42814317
Platform: ILLUMINA
Instrument: NextSeq 550
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 Flag-Zfp697
chip antibody: normal rabbit IgG (#2729, Cell Signaling)
geo_loc_name: missing
collection_date: missing
Original files (1)
mouse primary satellite cells
Runs (1)
| Run | Spots | Bases | Size (MB) | Files | Link |
|---|---|---|---|---|---|
| SRR29988224 | 66126321 | 8596421730 | 2610.16 | mIgG_CTRL1_S1_1.fastq.gz, mIgG_CTRL1_S1_2.fastq.gz, SRR29988224, SRR2… | SRA |
GSM8421743: Myotubes, Ad Flag-Zfp697, mIgG ab, rep2; Mus musculus; ChIP-Seq
Sample: SRS22124851
BioProject: PRJNA1140161
BioSample: SAMN42814316
Platform: ILLUMINA
Instrument: NextSeq 550
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 Flag-Zfp697
chip antibody: normal rabbit IgG (#2729, Cell Signaling)
geo_loc_name: missing
collection_date: missing
Original files (1)
mouse primary satellite cells
Runs (1)
| Run | Spots | Bases | Size (MB) | Files | Link |
|---|---|---|---|---|---|
| SRR29988223 | 47545723 | 6180943990 | 1892.94 | mIgG_CTRL2_S2_1.fastq.gz, mIgG_CTRL2_S2_2.fastq.gz, SRR29988223, SRR2… | SRA |
GSM8421744: Myotubes, Ad Flag-Zfp697, mIgG ab, rep3; Mus musculus; ChIP-Seq
Sample: SRS22124853
BioProject: PRJNA1140161
BioSample: SAMN42814315
Platform: ILLUMINA
Instrument: NextSeq 550
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 Flag-Zfp697
chip antibody: normal rabbit IgG (#2729, Cell Signaling)
geo_loc_name: missing
collection_date: missing
Original files (1)
mouse primary satellite cells
Runs (1)
| Run | Spots | Bases | Size (MB) | Files | Link |
|---|---|---|---|---|---|
| SRR29988222 | 70477164 | 9162031320 | 2795.67 | mIgG_CTRL3_S3_1.fastq.gz, mIgG_CTRL3_S3_2.fastq.gz, SRR29988222, SRR2… | 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 (8)
| Accession | File Name | Stored Type | Output Type | Mapping Assembly | Size | Download | |
|---|---|---|---|---|---|---|---|
| — | FLAG_1_S4_1.fastq.gz | ChIP-Seq | 1.2 GB | link | |||
| — | FLAG_2_S5_1.fastq.gz | ChIP-Seq | 3.1 GB | link | |||
| — | FLAG_3_S6_1.fastq.gz | ChIP-Seq | 3.2 GB | link | |||
| — | Input3_S7_1.fastq.gz | ChIP-Seq | 4.4 GB | link | |||
| — | mIgG_CTRL1_S1_1.fastq.gz | ChIP-Seq | 2.5 GB | link | |||
| — | mIgG_CTRL2_S2_1.fastq.gz | ChIP-Seq | 1.8 GB | link | |||
| — | mIgG_CTRL3_S3_1.fastq.gz | ChIP-Seq | 2.7 GB | link | |||
| — | SRR29988226.lite | ChIP-Seq | 3.2 GB | link |