NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM6696699 Query DataSets for GSM6696699
Status Public on Nov 02, 2022
Title After_1
Sample type SRA
 
Source name musculus soleus
Organism Homo sapiens
Characteristics tissue: musculus soleus
Sex: female
individual: 1
treatment: 3-day dry immersion
time point: after 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)
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model NextSeq 550
 
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
 
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
Relations
BioSample SAMN31513473
SRA SRX18070279

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap
External link. Please review our privacy policy.