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Status |
Public on Nov 02, 2022 |
Title |
Before_4 |
Sample type |
SRA |
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Source name |
musculus soleus
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Organism |
Homo sapiens |
Characteristics |
tissue: musculus soleus Sex: female individual: 4 treatment: No treatment time point: before treatment
|
Treatment protocol |
Six healthy females (25-39 years old [range]; median height 1.64 m and interquartile range [1.62-1.70] m; body mass 64.9 [60.8-67.9] kg; BMI 22.39 [20.19-24.59] kg/m2) were exposed to 3 days of “dry” immersion. Samples from the soleus muscle were taken prior to and after “dry” immersion from the left leg using a modified Bergström biopsy needle with manual suction under local anesthesia (2 ml 2% lidocaine). Both biopsies were taken on the 10-th day of the menstrual cycle.
|
Extracted molecule |
polyA RNA |
Extraction protocol |
A frozen muscle sample (~10-15 mg) was lysed by the RLT buffer (Qiagen, Germany) using a drill homogenizer and total RNA was extracted by a silica spin column (CleanRNA Standard, Evrogen, Russia). RNA concentration and integrity were evaluated by a fluorimetric assay (Qubit 4, ThermoScientific, USA) and capillary electrophoresis (TapeStation, Agilent, Germany), respectively. Strand-specific libraries were prepared by the NEBNext Ultra II Directional RNA Library Preparation kit (NEB, USA)
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
NextSeq 550 |
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Data processing |
Adapter sequences and low quality reads were trimmed using the Timmomatic tool (v0.36) (options:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:35) High-quality reads were aligned to the reference human GRCh38.p13 primary assembly genome using HISAT v2.1.0 Uniqe reads were counted for known exons of each gene using Rsubread package (R) and Ensembl annotation (GRCh38.101) TPM values calculated using kallisto v0.44.0 Assembly: GRCh38.p13 primary genome assembly Supplementary files format and content: tab-delimited text files: DESeq2.txt — differential expression analysis, Read_counts.txt — uniquely aligned read counts for genes
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Submission date |
Oct 28, 2022 |
Last update date |
Nov 02, 2022 |
Contact name |
Pavel Makhnovsky |
E-mail(s) |
maxpauel@gmail.com
|
Organization name |
Institute of Biomedical Problems of the Russian Academy of Sciences
|
Lab |
Laboratory of muscle physiology
|
Street address |
76A Khoroshevskoye shosse
|
City |
Moscow |
ZIP/Postal code |
123007 |
Country |
Russia |
|
|
Platform ID |
GPL21697 |
Series (1) |
GSE216845 |
Rapid changes in transcriptomic profile and mitochondrial function in human soleus muscle after three-day dry immersion |
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Relations |
BioSample |
SAMN31513468 |
SRA |
SRX18070284 |