GSE273092

GSE GEO

View on GEO Export SRA CSV

Zfp697 is an RNA-binding protein that regulates skeletal muscle inflammation and remodeling (Zfp697 skeletal muscle knockout RNA-Seq of unloading-reloading protocol)

Organism: Mus musculus

Platform: GPL24247

Samples: 18

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/PRJNA1140163

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 for mouse gastrocnemius muscle from model of hindlimb unloading/reloading comparing wild-type and Zfp697 conditional skeletal muscle knockout (mKO) animals. Control mice were kept in conventional cages throughout the entire protocol. Experiment was performed in three replicates per condition.

Analysis (3 steps)

View Data Processing

Processing steps for GSE273092

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 --outFilterScoreMinOverLread 0 --outFilterMatchNmin 0 --outFilterMatchNminOverLread 0 --outFilterMismatchNmax 33 --seedSearchStartLmax 12 --alignSJoverhangMin 8 --alignEndsType Local
Reads aligning to gene exons (Mus_musculus.GRCm38.94.gtf) were counted using featureCounts v2.0.3 program from Subread package, summarized at gene level.
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 (5)

GSE273092_featureCounts_output.txt.gz Download

GSE273092_zfp697_mKO_control_vs_wt_control_deseq2.txt.gz Download

GSE273092_zfp697_mKO_reloading_vs_control_deseq2.txt.gz Download

GSE273092_zfp697_mKO_reloading_vs_unloading_deseq2.txt.gz Download

GSE273092_zfp697_mKO_unloading_vs_control_deseq2.txt.gz Download

GEO Samples (18)

GSM8421714 GSM8421715 GSM8421716 GSM8421717 GSM8421718 GSM8421719 GSM8421720 GSM8421721 GSM8421722 GSM8421723 GSM8421724 GSM8421725 GSM8421726 GSM8421727 GSM8421728 GSM8421729 GSM8421730 GSM8421731

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 (18) and Runs (18)

Total: 31689 MB

SRX25468523 SRP522174 RNA-Seq PAIRED

GSM8421714: Muscle, flox/flox, control, rep1; Mus musculus; RNA-Seq

Sample: SRS22124878

BioProject: PRJNA1140163

BioSample: SAMN42814352

Platform: ILLUMINA

Instrument: Illumina NovaSeq 6000

Organism: Mus musculus

Sample attributes

source_name: gastrocnemius skeletal muscle

strain: C57BL/6

Sex: female

tissue: gastrocnemius skeletal muscle

genotype: flox

intervention: ctrl

geo_loc_name: missing

collection_date: missing

Original files (1)

gastrocnemius skeletal muscle

Runs (1)

Run	Spots	Bases	Size (MB)	Files	Link
SRR29988480	31517362	6334989762	1807.38	JR-JC-1_1.fastq.gz, JR-JC-1_2.fastq.gz, SRR29988480, SRR29988480.lite	SRA

SRX25468524 SRP522174 RNA-Seq PAIRED

GSM8421715: Muscle, flox/flox, control, rep2; Mus musculus; RNA-Seq

Sample: SRS22124888

BioProject: PRJNA1140163

BioSample: SAMN42814351

Platform: ILLUMINA

Instrument: Illumina NovaSeq 6000

Organism: Mus musculus

Sample attributes

source_name: gastrocnemius skeletal muscle

strain: C57BL/6

Sex: female

tissue: gastrocnemius skeletal muscle

genotype: flox

intervention: ctrl

geo_loc_name: missing

collection_date: missing

Original files (1)

gastrocnemius skeletal muscle

Runs (1)

Run	Spots	Bases	Size (MB)	Files	Link
SRR29988479	29840357	5997911757	1712.59	JR-JC-2_1.fastq.gz, JR-JC-2_2.fastq.gz, SRR29988479, SRR29988479.lite	SRA

SRX25468525 SRP522174 RNA-Seq PAIRED

GSM8421716: Muscle, flox/flox, control, rep3; Mus musculus; RNA-Seq

Sample: SRS22124881

BioProject: PRJNA1140163

BioSample: SAMN42814350

Platform: ILLUMINA

Instrument: Illumina NovaSeq 6000

Organism: Mus musculus

Sample attributes

source_name: gastrocnemius skeletal muscle

strain: C57BL/6

Sex: female

tissue: gastrocnemius skeletal muscle

genotype: flox

intervention: ctrl

geo_loc_name: missing

collection_date: missing

Original files (1)

gastrocnemius skeletal muscle

Runs (1)

Run	Spots	Bases	Size (MB)	Files	Link
SRR29988478	29151118	5859374718	1673.52	JR-JC-3_1.fastq.gz, JR-JC-3_2.fastq.gz, SRR29988478, SRR29988478.lite	SRA

SRX25468526 SRP522174 RNA-Seq PAIRED

GSM8421717: Muscle, Zfp697 mKO, control, rep1; Mus musculus; RNA-Seq

Sample: SRS22124880

BioProject: PRJNA1140163

BioSample: SAMN42814349

Platform: ILLUMINA

Instrument: Illumina NovaSeq 6000

Organism: Mus musculus

Sample attributes

source_name: gastrocnemius skeletal muscle

strain: C57BL/6

Sex: female

tissue: gastrocnemius skeletal muscle

genotype: mKO

intervention: ctrl

geo_loc_name: missing

collection_date: missing

Original files (1)

gastrocnemius skeletal muscle

Runs (1)

Run	Spots	Bases	Size (MB)	Files	Link
SRR29988477	30825729	6195971529	1764.45	JR-JC-4_1.fastq.gz, JR-JC-4_2.fastq.gz, SRR29988477, SRR29988477.lite	SRA

SRX25468527 SRP522174 RNA-Seq PAIRED

GSM8421718: Muscle, Zfp697 mKO, control, rep2; Mus musculus; RNA-Seq

Sample: SRS22124884

BioProject: PRJNA1140163

BioSample: SAMN42814348

Platform: ILLUMINA

Instrument: Illumina NovaSeq 6000

Organism: Mus musculus

Sample attributes

source_name: gastrocnemius skeletal muscle

strain: C57BL/6

Sex: female

tissue: gastrocnemius skeletal muscle

genotype: mKO

intervention: ctrl

geo_loc_name: missing

collection_date: missing

Original files (1)

gastrocnemius skeletal muscle

Runs (1)

Run	Spots	Bases	Size (MB)	Files	Link
SRR29988476	32735358	6579806958	1872.84	JR-JC-5_1.fastq.gz, JR-JC-5_2.fastq.gz, SRR29988476, SRR29988476.lite	SRA

SRX25468528 SRP522174 RNA-Seq PAIRED

GSM8421719: Muscle, Zfp697 mKO, control, rep3; Mus musculus; RNA-Seq

Sample: SRS22124885

BioProject: PRJNA1140163

BioSample: SAMN42814347

Platform: ILLUMINA

Instrument: Illumina NovaSeq 6000

Organism: Mus musculus

Sample attributes

source_name: gastrocnemius skeletal muscle

strain: C57BL/6

Sex: female

tissue: gastrocnemius skeletal muscle

genotype: mKO

intervention: ctrl

geo_loc_name: missing

collection_date: missing

Original files (1)

gastrocnemius skeletal muscle

Runs (1)

Run	Spots	Bases	Size (MB)	Files	Link
SRR29988475	31050720	6241194720	1783.3	JR-JC-6_1.fastq.gz, JR-JC-6_2.fastq.gz, SRR29988475, SRR29988475.lite	SRA

SRX25468529 SRP522174 RNA-Seq PAIRED

GSM8421720: Muscle, flox/flox, unloading 10 days, rep1; Mus musculus; RNA-Seq

Sample: SRS22124889

BioProject: PRJNA1140163

BioSample: SAMN42814346

Platform: ILLUMINA

Instrument: Illumina NovaSeq 6000

Organism: Mus musculus

Sample attributes

source_name: gastrocnemius skeletal muscle

strain: C57BL/6

Sex: female

tissue: gastrocnemius skeletal muscle

genotype: flox

intervention: unloading_10days

geo_loc_name: missing

collection_date: missing

Original files (1)

gastrocnemius skeletal muscle

Runs (1)

Run	Spots	Bases	Size (MB)	Files	Link
SRR29988474	30999685	6230936685	1773.76	JR-JC-7_1.fastq.gz, JR-JC-7_2.fastq.gz, SRR29988474, SRR29988474.lite	SRA

SRX25468530 SRP522174 RNA-Seq PAIRED

GSM8421721: Muscle, flox/flox, unloading 10 days, rep2; Mus musculus; RNA-Seq

Sample: SRS22124883

BioProject: PRJNA1140163

BioSample: SAMN42814345

Platform: ILLUMINA

Instrument: Illumina NovaSeq 6000

Organism: Mus musculus

Sample attributes

source_name: gastrocnemius skeletal muscle

strain: C57BL/6

Sex: female

tissue: gastrocnemius skeletal muscle

genotype: flox

intervention: unloading_10days

geo_loc_name: missing

collection_date: missing

Original files (1)

gastrocnemius skeletal muscle

Runs (1)

Run	Spots	Bases	Size (MB)	Files	Link
SRR29988473	30414361	6113286561	1743.59	JR-JC-8_1.fastq.gz, JR-JC-8_2.fastq.gz, SRR29988473, SRR29988473.lite	SRA

SRX25468531 SRP522174 RNA-Seq PAIRED

GSM8421722: Muscle, flox/flox, unloading 10 days, rep3; Mus musculus; RNA-Seq

Sample: SRS22124886

BioProject: PRJNA1140163

BioSample: SAMN42814344

Platform: ILLUMINA

Instrument: Illumina NovaSeq 6000

Organism: Mus musculus

Sample attributes

source_name: gastrocnemius skeletal muscle

strain: C57BL/6

Sex: female

tissue: gastrocnemius skeletal muscle

genotype: flox

intervention: unloading_10days

geo_loc_name: missing

collection_date: missing

Original files (1)

gastrocnemius skeletal muscle

Runs (1)

Run	Spots	Bases	Size (MB)	Files	Link
SRR29988472	31980499	6428080299	1827.65	SRR29988472.lite, SRR29988472, JR-JC-9_2.fastq.gz, JR-JC-9_1.fastq.gz	SRA

SRX25468532 SRP522174 RNA-Seq PAIRED

GSM8421723: Muscle, Zfp697 mKO, unloading 10 days, rep1; Mus musculus; RNA-Seq

Sample: SRS22124887

BioProject: PRJNA1140163

BioSample: SAMN42814343

Platform: ILLUMINA

Instrument: Illumina NovaSeq 6000

Organism: Mus musculus

Sample attributes

source_name: gastrocnemius skeletal muscle

strain: C57BL/6

Sex: female

tissue: gastrocnemius skeletal muscle

genotype: mKO

intervention: unloading_10days

geo_loc_name: missing

collection_date: missing

Original files (1)

gastrocnemius skeletal muscle

Runs (1)

Run	Spots	Bases	Size (MB)	Files	Link
SRR29988471	29734661	5976666861	1709.7	JR-JC-10_1.fastq.gz, JR-JC-10_2.fastq.gz, SRR29988471, SRR29988471.li…	SRA

SRX25468533 SRP522174 RNA-Seq PAIRED

GSM8421724: Muscle, Zfp697 mKO, unloading 10 days, rep2; Mus musculus; RNA-Seq

Sample: SRS22124890

BioProject: PRJNA1140163

BioSample: SAMN42814342

Platform: ILLUMINA

Instrument: Illumina NovaSeq 6000

Organism: Mus musculus

Sample attributes

source_name: gastrocnemius skeletal muscle

strain: C57BL/6

Sex: female

tissue: gastrocnemius skeletal muscle

genotype: mKO

intervention: unloading_10days

geo_loc_name: missing

collection_date: missing

Original files (1)

gastrocnemius skeletal muscle

Runs (1)

Run	Spots	Bases	Size (MB)	Files	Link
SRR29988470	29007475	5830502475	1661.28	JR-JC-11_1.fastq.gz, JR-JC-11_2.fastq.gz, SRR29988470, SRR29988470.li…	SRA

SRX25468534 SRP522174 RNA-Seq PAIRED

GSM8421725: Muscle, Zfp697 mKO, unloading 10 days, rep3; Mus musculus; RNA-Seq

Sample: SRS22124892

BioProject: PRJNA1140163

BioSample: SAMN42814341

Platform: ILLUMINA

Instrument: Illumina NovaSeq 6000

Organism: Mus musculus

Sample attributes

source_name: gastrocnemius skeletal muscle

strain: C57BL/6

Sex: female

tissue: gastrocnemius skeletal muscle

genotype: mKO

intervention: unloading_10days

geo_loc_name: missing

collection_date: missing

Original files (1)

gastrocnemius skeletal muscle

Runs (1)

Run	Spots	Bases	Size (MB)	Files	Link
SRR29988469	31299738	6291247338	1792.81	JR-JC-12_1.fastq.gz, JR-JC-12_2.fastq.gz, SRR29988469, SRR29988469.li…	SRA

SRX25468535 SRP522174 RNA-Seq PAIRED

GSM8421726: Muscle, flox/flox, reloading 3 days, rep1; Mus musculus; RNA-Seq

Sample: SRS22124891

BioProject: PRJNA1140163

BioSample: SAMN42814340

Platform: ILLUMINA

Instrument: Illumina NovaSeq 6000

Organism: Mus musculus

Sample attributes

source_name: gastrocnemius skeletal muscle

strain: C57BL/6

Sex: female

tissue: gastrocnemius skeletal muscle

genotype: flox

intervention: reloading_3days

geo_loc_name: missing

collection_date: missing

Original files (1)

gastrocnemius skeletal muscle

Runs (1)

Run	Spots	Bases	Size (MB)	Files	Link
SRR29988468	28971421	5823255621	1662.29	JR-JC-13_1.fastq.gz, JR-JC-13_2.fastq.gz, SRR29988468, SRR29988468.li…	SRA

SRX25468536 SRP522174 RNA-Seq PAIRED

GSM8421727: Muscle, flox/flox, reloading 3 days, rep2; Mus musculus; RNA-Seq

Sample: SRS22124893

BioProject: PRJNA1140163

BioSample: SAMN42814339

Platform: ILLUMINA

Instrument: Illumina NovaSeq 6000

Organism: Mus musculus

Sample attributes

source_name: gastrocnemius skeletal muscle

strain: C57BL/6

Sex: female

tissue: gastrocnemius skeletal muscle

genotype: flox

intervention: reloading_3days

geo_loc_name: missing

collection_date: missing

Original files (1)

gastrocnemius skeletal muscle

Runs (1)

Run	Spots	Bases	Size (MB)	Files	Link
SRR29988467	30816996	6194216196	1767.61	JR-JC-14_1.fastq.gz, JR-JC-14_2.fastq.gz, SRR29988467, SRR29988467.li…	SRA

SRX25468537 SRP522174 RNA-Seq PAIRED

GSM8421728: Muscle, flox/flox, reloading 3 days, rep3; Mus musculus; RNA-Seq

Sample: SRS22124895

BioProject: PRJNA1140163

BioSample: SAMN42814338

Platform: ILLUMINA

Instrument: Illumina NovaSeq 6000

Organism: Mus musculus

Sample attributes

source_name: gastrocnemius skeletal muscle

strain: C57BL/6

Sex: female

tissue: gastrocnemius skeletal muscle

genotype: flox

intervention: reloading_3days

geo_loc_name: missing

collection_date: missing

Original files (1)

gastrocnemius skeletal muscle

Runs (1)

Run	Spots	Bases	Size (MB)	Files	Link
SRR29988466	30844285	6199701285	1765.89	JR-JC-15_1.fastq.gz, JR-JC-15_2.fastq.gz, SRR29988466, SRR29988466.li…	SRA

SRX25468538 SRP522174 RNA-Seq PAIRED

GSM8421729: Muscle, Zfp697 mKO, reloading 3 days, rep1; Mus musculus; RNA-Seq

Sample: SRS22124894

BioProject: PRJNA1140163

BioSample: SAMN42814337

Platform: ILLUMINA

Instrument: Illumina NovaSeq 6000

Organism: Mus musculus

Sample attributes

source_name: gastrocnemius skeletal muscle

strain: C57BL/6

Sex: female

tissue: gastrocnemius skeletal muscle

genotype: mKO

intervention: reloading_3days

geo_loc_name: missing

collection_date: missing

Original files (1)

gastrocnemius skeletal muscle

Runs (1)

Run	Spots	Bases	Size (MB)	Files	Link
SRR29988465	29329854	5895300654	1690.13	JR-JC-16_1.fastq.gz, JR-JC-16_2.fastq.gz, SRR29988465, SRR29988465.li…	SRA

SRX25468539 SRP522174 RNA-Seq PAIRED

GSM8421730: Muscle, Zfp697 mKO, reloading 3 days, rep2; Mus musculus; RNA-Seq

Sample: SRS22124901

BioProject: PRJNA1140163

BioSample: SAMN42814336

Platform: ILLUMINA

Instrument: Illumina NovaSeq 6000

Organism: Mus musculus

Sample attributes

source_name: gastrocnemius skeletal muscle

strain: C57BL/6

Sex: female

tissue: gastrocnemius skeletal muscle

genotype: mKO

intervention: reloading_3days

geo_loc_name: missing

collection_date: missing

Original files (1)

gastrocnemius skeletal muscle

Runs (1)

Run	Spots	Bases	Size (MB)	Files	Link
SRR29988464	31677826	6367243026	1820.06	JR-JC-17_1.fastq.gz, JR-JC-17_2.fastq.gz, SRR29988464, SRR29988464.li…	SRA

SRX25468540 SRP522174 RNA-Seq PAIRED

GSM8421731: Muscle, Zfp697 mKO, reloading 3 days, rep3; Mus musculus; RNA-Seq

Sample: SRS22124896

BioProject: PRJNA1140163

BioSample: SAMN42814335

Platform: ILLUMINA

Instrument: Illumina NovaSeq 6000

Organism: Mus musculus

Sample attributes

source_name: gastrocnemius skeletal muscle

strain: C57BL/6

Sex: female

tissue: gastrocnemius skeletal muscle

genotype: mKO

intervention: reloading_3days

geo_loc_name: missing

collection_date: missing

Original files (1)

gastrocnemius skeletal muscle

Runs (1)

Run	Spots	Bases	Size (MB)	Files	Link
SRR29988463	32442075	6520857075	1860.37	JR-JC-18_1.fastq.gz, JR-JC-18_2.fastq.gz, SRR29988463, SRR29988463.li…	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 (19)

Accession	File Name	Stored Type	Size	Download
—	JR-JC-10_1.fastq.gz	RNA-Seq	1.7 GB	link
—	JR-JC-11_1.fastq.gz	RNA-Seq	1.6 GB	link
—	JR-JC-1_1.fastq.gz	RNA-Seq	1.8 GB	link
—	JR-JC-12_1.fastq.gz	RNA-Seq	1.8 GB	link
—	JR-JC-13_1.fastq.gz	RNA-Seq	1.6 GB	link
—	JR-JC-14_1.fastq.gz	RNA-Seq	1.7 GB	link
—	JR-JC-15_1.fastq.gz	RNA-Seq	1.7 GB	link
—	JR-JC-16_1.fastq.gz	RNA-Seq	1.7 GB	link
—	JR-JC-17_1.fastq.gz	RNA-Seq	1.8 GB	link
—	JR-JC-18_1.fastq.gz	RNA-Seq	1.8 GB	link
—	JR-JC-2_1.fastq.gz	RNA-Seq	1.7 GB	link
—	JR-JC-3_1.fastq.gz	RNA-Seq	1.6 GB	link
—	JR-JC-4_1.fastq.gz	RNA-Seq	1.7 GB	link
—	JR-JC-5_1.fastq.gz	RNA-Seq	1.8 GB	link
—	JR-JC-6_1.fastq.gz	RNA-Seq	1.7 GB	link
—	JR-JC-7_1.fastq.gz	RNA-Seq	1.7 GB	link
—	JR-JC-8_1.fastq.gz	RNA-Seq	1.7 GB	link
—	JR-JC-9_1.fastq.gz	RNA-Seq	1.8 GB	link
—	SRR29988472.lite	RNA-Seq	1.8 GB	link