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| Status |
Public on May 05, 2023 |
| Title |
H_before_MMTT_2 |
| Sample type |
SRA |
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| Source name |
musculus vastus lateralis
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| Organism |
Homo sapiens |
| Characteristics |
tissue: musculus vastus lateralis
Sex: male
individual: 9
treatment: No treatment
time point: before treatment
age: 59
diagnosis: Metabolically healthy
bmi: 23.5
fasting glucose,_mm: 5.27
fasting insulin,_miu/l: 7.2
fasting c-peptid,_ng/ml: 2.23
hba1c, %: 5.5
homa ir: 1.7
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| 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.
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| 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: Read_counts.txt — uniquely aligned read counts for genes
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| Submission date |
May 02, 2023 |
| Last update date |
May 05, 2023 |
| Contact name |
Pavel Makhnovsky |
| E-mail(s) |
maxpauel@gmail.com
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| Organization name |
Institute of Biomedical Problems of the Russian Academy of Sciences
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| Lab |
Laboratory of muscle physiology
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| Street address |
76A Khoroshevskoye shosse
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| City |
Moscow |
| ZIP/Postal code |
123007 |
| Country |
Russia |
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| Platform ID |
GPL21697 |
| Series (1) |
| GSE231509 |
Dysregulation of mixed meal-induced gene expression in skeletal muscle in obesity and type 2 diabetes |
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| Relations |
| BioSample |
SAMN34536362 |
| SRA |
SRX20191093 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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