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| Status |
Public on Oct 31, 2024 |
| Title |
Skeletal muscle, C57_GL2 |
| Sample type |
SRA |
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| Source name |
Skeletal muscle
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| Organism |
Mus musculus |
| Characteristics |
tissue: Skeletal muscle
strain: C57BL/6
Sex: Male
genotype: WT
treatment: neuron-denervated (Den); left leg muscles (Healthy)
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| Treatment protocol |
The mice were anesthetized with inhaled isoflurane, placed on the operating table in the prone position, and the skin was prepared in the surgical area of the right hind limb; a surgical incision of 6-8 mm in length was made in the middle of the right posterior femur to expose the biceps femoris muscle and the pyriformis muscle, and bluntly isolate and expose the sciatic nerve; the sciatic nerve was cut 1 cm below the lower edge of the pyriformis muscle, and a notch of 1.5 cm was prepared in each end; the two severed ends of the nerves were turned over by 180° and sutured to the adjacent muscle tissue, and the muscle and skin were sutured layer by layer. In the sham-operated group, only the sciatic nerve was exposed, but no nerve amputation was performed. Two weeks after surgery, the gastrocnemius muscle was selected for the experiment.
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| Growth protocol |
Mice were maintained under standard housing conditions and received a regular diet.
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total cellular RNA was extracted using the RNA Rapid Extraction Kit (Vazyme, Nanjing, China) and total tissue RNA was extracted using Trizol (Vazyme), according to the reagent instructions.
The RNA-seq library preparation was followed by the instructions of LC Bio Technology CO., Ltd.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
BGISEQ-500 |
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| Description |
mice_muscle_C57_LR_RNA_seq_rpkm.txt
CGL2A
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| Data processing |
RNA-seq raw files (fastq, SE50) were aligned to the GRCm38/mm10 version of the mouse reference genome, using HISAT2 with default parameters. Read counts were imported by HOMER and analyzed using analyzeRepeats with the option rna and parameters -noadj -condenseGenes and -count exons for four replicates per condition. Differential gene expression was performed with DESeq2 using HOMER’s getDiffExpression.pl using default parameter. Transcripts with an adjusted p-value < 0.05 were considered as differentially expressed genes.
HISAT2
DESeq2
HOMER
Adjusted p-value < 0.05
Assembly: GRCm38/mm10
Supplementary files format and content: Bedgraph files contain the gene expression tags counts and p-value.
Supplementary files format and content: The differential expression file was further provided (tab-delimited file).
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| Submission date |
Jan 17, 2024 |
| Last update date |
Oct 31, 2024 |
| Contact name |
Zhiqiang Huang |
| E-mail(s) |
zhiqiang.huang@ki.se, zhiqiang.huang@nju.edu.cn
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| Organization name |
Nanjing University
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| Department |
Medical School
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| Street address |
Hankou 22
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| City |
Nanjing |
| State/province |
Jiangsu |
| ZIP/Postal code |
210093 |
| Country |
China |
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| Platform ID |
GPL23479 |
| Series (1) |
| GSE253469 |
Effects of Denervation on Muscle Function |
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| Relations |
| BioSample |
SAMN39473960 |
| SRA |
SRX23266775 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM8021181_C57_GL2.ucsc.bedGraph.gz |
37.4 Mb |
(ftp)(http) |
BEDGRAPH |
SRA Run Selector |
| Raw data are available in SRA |
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