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GSE237099

GSE GEO
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Analysis of skeletal muscle gene expression upon mouse hindlimb unloading and reloading

Organism: Mus musculus
Platform: GPL13112
Samples: 9
Experiment Types:
Expression profiling by high throughput sequencing
Submitted: Jul 11 2023
Last Updated: Jan 21 2026
Status: Public on Jul 16 2023
Contact: Igor,,Cervenka (Karolinska Institutet)

Relations

BioProject: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA993705

Summary

To investigate the molecular mechanisms governing the transition of skeletal muscle from atrophy to compensatory regeneration and hypertrophy, we employed a mouse model involving hindlimb unloading and subsequent reloading, conducting a comprehensive analysis of global gene expression using RNA-sequencing (RNA-seq). Gastrocnemius muscle samples were obtained from three groups: control mice, mice subjected to 10 days of hindlimb unloading-induced muscle atrophy, and mice reintroduced to normal cage activity for 1 day following the unloading period (reloading).

Overall Design

Comparative gene expression profiling analysis of RNA-seq data for mouse gastrocnemius muscle from model of hindlimb unloading/reloading assessing transitions from atrophy to compensatory regeneration and hypertrophy. Control mice were kept in conventional cages throughout the entire protocol. Experiment was performed in replicates (Control n = 4, Unloading n = 2, Reloading n = 3). Paired-end DNA libraries were prepared using Illumina TrueSeq and sequenced on Illumina HiSeq2000 (.

Analysis (3 steps)

View Data Processing
Processing steps for GSE237099
  1. 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 parameters --outFilterScoreMinOverLread 0 --outFilterMatchNmin 0 --outFilterMatchNminOverLread 0 --outFilterMismatchNmax 33 --seedSearchStartLmax 12 --alignSJoverhangMin 8
  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 --countReadPairs.
  3. 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 (4)

GSE237099_1_unloading_reloading_Reloading_vs_Control_deseq2.txt.gz Download
GSE237099_1_unloading_reloading_Reloading_vs_Unloading_deseq2.txt.gz Download
GSE237099_1_unloading_reloading_Unloading_vs_Control_deseq2.txt.gz Download
GSE237099_featureCounts_output.txt.gz Download
GEO Samples (9)
GSM7594876 GSM7594877 GSM7594878 GSM7594879 GSM7594880 GSM7594881 GSM7594882 GSM7594883 GSM7594884

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 (9) and Runs (9)

Total: 18669 MB
SRX20984694 SRP448625 RNA-Seq PAIRED
GSM7594876: Muscle, control, rep1; Mus musculus; RNA-Seq
Sample: SRS18259813
BioProject: PRJNA993705
BioSample: SAMN36408279
Platform: ILLUMINA
Instrument: Illumina HiSeq 2000
Organism: Mus musculus
Sample attributes
source_name: gastrocnemium skeletal muscle
strain: C57BL/6
Sex: male
tissue: gastrocnemium skeletal muscle
genotype: wild-type
intervention: control
geo_loc_name: missing
collection_date: missing
Original files (1)
gastrocnemium skeletal muscle
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR25238424 11900137 2403827674 1465.92 ctrl_1_1.fastq.gz, ctrl_1_2.fastq.gz, SRR25238424, SRR25238424.lite SRA
SRX20984695 SRP448625 RNA-Seq PAIRED
GSM7594877: Muscle, control, rep2; Mus musculus; RNA-Seq
Sample: SRS18259814
BioProject: PRJNA993705
BioSample: SAMN36408278
Platform: ILLUMINA
Instrument: Illumina HiSeq 2000
Organism: Mus musculus
Sample attributes
source_name: gastrocnemium skeletal muscle
strain: C57BL/6
Sex: male
tissue: gastrocnemium skeletal muscle
genotype: wild-type
intervention: control
geo_loc_name: missing
collection_date: missing
Original files (1)
gastrocnemium skeletal muscle
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR25238423 16244738 3281437076 1992.53 ctrl_2_1.fastq.gz, ctrl_2_2.fastq.gz, SRR25238423, SRR25238423.lite SRA
SRX20984696 SRP448625 RNA-Seq PAIRED
GSM7594878: Muscle, control, rep3; Mus musculus; RNA-Seq
Sample: SRS18259815
BioProject: PRJNA993705
BioSample: SAMN36408277
Platform: ILLUMINA
Instrument: Illumina HiSeq 2000
Organism: Mus musculus
Sample attributes
source_name: gastrocnemium skeletal muscle
strain: C57BL/6
Sex: male
tissue: gastrocnemium skeletal muscle
genotype: wild-type
intervention: control
geo_loc_name: missing
collection_date: missing
Original files (1)
gastrocnemium skeletal muscle
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR25238422 18742400 3785964800 2301.75 ctrl_3_1.fastq.gz, ctrl_3_2.fastq.gz, SRR25238422, SRR25238422.lite SRA
SRX20984697 SRP448625 RNA-Seq PAIRED
GSM7594879: Muscle, control, rep4; Mus musculus; RNA-Seq
Sample: SRS18259817
BioProject: PRJNA993705
BioSample: SAMN36408276
Platform: ILLUMINA
Instrument: Illumina HiSeq 2000
Organism: Mus musculus
Sample attributes
source_name: gastrocnemium skeletal muscle
strain: C57BL/6
Sex: male
tissue: gastrocnemium skeletal muscle
genotype: wild-type
intervention: control
geo_loc_name: missing
collection_date: missing
Original files (1)
gastrocnemium skeletal muscle
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR25238421 15981898 3228343396 1973.93 ctrl_4_1.fastq.gz, ctrl_4_2.fastq.gz, SRR25238421, SRR25238421.lite SRA
SRX20984698 SRP448625 RNA-Seq PAIRED
GSM7594880: Muscle, reloading day 1, rep1; Mus musculus; RNA-Seq
Sample: SRS18259818
BioProject: PRJNA993705
BioSample: SAMN36408275
Platform: ILLUMINA
Instrument: Illumina HiSeq 2000
Organism: Mus musculus
Sample attributes
source_name: gastrocnemium skeletal muscle
strain: C57BL/6
Sex: male
tissue: gastrocnemium skeletal muscle
genotype: wild-type
intervention: reloading_day1
geo_loc_name: missing
collection_date: missing
Original files (1)
gastrocnemium skeletal muscle
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR25238420 13829282 2793514964 1699.2 rel_2_1.fastq.gz, rel_2_2.fastq.gz, SRR25238420, SRR25238420.lite SRA
SRX20984699 SRP448625 RNA-Seq PAIRED
GSM7594881: Muscle, reloading day 1, rep2; Mus musculus; RNA-Seq
Sample: SRS18259825
BioProject: PRJNA993705
BioSample: SAMN36408274
Platform: ILLUMINA
Instrument: Illumina HiSeq 2000
Organism: Mus musculus
Sample attributes
source_name: gastrocnemium skeletal muscle
strain: C57BL/6
Sex: male
tissue: gastrocnemium skeletal muscle
genotype: wild-type
intervention: reloading_day1
geo_loc_name: missing
collection_date: missing
Original files (1)
gastrocnemium skeletal muscle
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR25238419 15480693 3127099986 1907.75 rel_3_1.fastq.gz, rel_3_2.fastq.gz, SRR25238419, SRR25238419.lite SRA
SRX20984700 SRP448625 RNA-Seq PAIRED
GSM7594882: Muscle, reloading day 1, rep3; Mus musculus; RNA-Seq
Sample: SRS18259819
BioProject: PRJNA993705
BioSample: SAMN36408273
Platform: ILLUMINA
Instrument: Illumina HiSeq 2000
Organism: Mus musculus
Sample attributes
source_name: gastrocnemium skeletal muscle
strain: C57BL/6
Sex: male
tissue: gastrocnemium skeletal muscle
genotype: wild-type
intervention: reloading_day1
geo_loc_name: missing
collection_date: missing
Original files (1)
gastrocnemium skeletal muscle
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR25238418 17057550 3445625100 2093.6 rel_4_1.fastq.gz, rel_4_2.fastq.gz, SRR25238418, SRR25238418.lite SRA
SRX20984701 SRP448625 RNA-Seq PAIRED
GSM7594883: Muscle, hindlimb unloading day 10, rep1; Mus musculus; RNA-Seq
Sample: SRS18259820
BioProject: PRJNA993705
BioSample: SAMN36408272
Platform: ILLUMINA
Instrument: Illumina HiSeq 2000
Organism: Mus musculus
Sample attributes
source_name: gastrocnemium skeletal muscle
strain: C57BL/6
Sex: male
tissue: gastrocnemium skeletal muscle
genotype: wild-type
intervention: unloading_day10
geo_loc_name: missing
collection_date: missing
Original files (1)
gastrocnemium skeletal muscle
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR25238417 17670122 3569364644 2193.23 sus_1_1.fastq.gz, sus_1_2.fastq.gz, SRR25238417, SRR25238417.lite SRA
SRX20984702 SRP448625 RNA-Seq PAIRED
GSM7594884: Muscle, hindlimb unloading day 10, rep2; Mus musculus; RNA-Seq
Sample: SRS18259821
BioProject: PRJNA993705
BioSample: SAMN36408271
Platform: ILLUMINA
Instrument: Illumina HiSeq 2000
Organism: Mus musculus
Sample attributes
source_name: gastrocnemium skeletal muscle
strain: C57BL/6
Sex: male
tissue: gastrocnemium skeletal muscle
genotype: wild-type
intervention: unloading_day10
geo_loc_name: missing
collection_date: missing
Original files (1)
gastrocnemium skeletal muscle
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR25238416 24614081 4972044362 3041.38 sus_2_1.fastq.gz, sus_2_2.fastq.gz, SRR25238416, SRR25238416.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 (9)

Accession File Name Stored Type Output Type Mapping Assembly Size Download
— ctrl_1_1.fastq.gz RNA-Seq 1.4 GB link
— ctrl_2_1.fastq.gz RNA-Seq 1.9 GB link
— ctrl_3_1.fastq.gz RNA-Seq 2.2 GB link
— ctrl_4_1.fastq.gz RNA-Seq 1.9 GB link
— rel_2_1.fastq.gz RNA-Seq 1.7 GB link
— rel_3_1.fastq.gz RNA-Seq 1.9 GB link
— rel_4_1.fastq.gz RNA-Seq 2.0 GB link
— sus_1_1.fastq.gz RNA-Seq 2.1 GB link
— sus_2_1.fastq.gz RNA-Seq 3.0 GB link