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Sample GSM7287000 Query DataSets for GSM7287000
Status Public on May 05, 2023
Title H_before_MMTT_5
Sample type SRA
Source name musculus vastus lateralis
Organism Homo sapiens
Characteristics tissue: musculus vastus lateralis
Sex: female
individual: 12
treatment: No treatment
time point: before treatment
age: 41
diagnosis: Metabolically healthy
bmi: 18.9
fasting glucose,_mm: 4.43
fasting insulin,_miu/l: 7.52
fasting c-peptid,_ng/ml: 1.91
hba1c, %: 5.3
homa ir: 1.5
Treatment protocol Seven healthy subjects, 7 obese patients, and 7 obese patients with T2D were involved in the study. Subjects arrived at the laboratory at 09:00 after 12 h overnight fast. The venous blood was drawn from the v. intermedia cubiti using catheter prior to, and at 30, and 60 min after the mixed meal tolerant test (MMTT; nutritional drink Resource 2.0 [Nestle Health Science, France], 3 ml/kg of body mass, protein:lipid:carbohydrate 9:9:21, 840 kJ/100 ml). The plasma concentration of glucose and glycated hemoglobin was evaluated using an automatic analyzer Architect c8000 (Abbott Diagnostics, USA) and by HPLC (analyzer D10, BioRad, USA); the serum concentration of insulin and C-peptide was evaluated using an automatic analyzer Cobas 6000 (Roche, Switzerland). Biopsy samples were taken under local anesthesia (2 ml 2% lidocaine) using a modified Bergström needle with manual suction from the left vastus lateralis muscle prior to and after the MMTT.
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: Read_counts.txt — uniquely aligned read counts for genes
Submission date May 02, 2023
Last update date May 05, 2023
Contact name Pavel Makhnovsky
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)
GSE231509 Dysregulation of mixed meal-induced gene expression in skeletal muscle in obesity and type 2 diabetes
BioSample SAMN34536356
SRA SRX20191099

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

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