|
Status |
Public on Jul 05, 2020 |
Title |
14_1 |
Sample type |
SRA |
|
|
Source name |
Venous blood sample
|
Organism |
Homo sapiens |
Characteristics |
patient diagnosis: type 2 diabetes mellitus tissue: blood time point of blood collcetion regarding metformin intervention: before administration of metformin
|
Treatment protocol |
Venous blood samples were collected in Tempus™ Blood RNA Tubes (ThermoFisher Scientific), containing Stabilizing Reagent.
|
Extracted molecule |
total RNA |
Extraction protocol |
Total RNA isolation was performed with Tempus™ Spin RNA Isolation Kit (Thermo Fisher Scientific), according to the manufacturer's instructions. Ribosomal RNA depletion was done with Low Input RiboMinus™ Eukaryote System v2 (Thermo Fisher Scientific, USA) by processing 500ng of total RNA from each sample. For cDNA library preparation we used Ion Total RNA-Seq Kit v2 (Thermo Fisher Scientific, USA), sequencing was done on Ion Proton™ System and Ion PI™ Chip (Thermo Fisher Scientific, USA), following the manufacturer’s instructions.
|
|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Ion Torrent Proton |
|
|
Description |
Ion Torrent, Ion Proton System
|
Data processing |
The reads were trimmed with Trimmomatic 0.36 using window size 5 and quality threshold 10. Sequencing reads were mapped against human reference genome GRCh38 release 90 and read counts were calculated with STAR 2.5.3a. Genome_build: GRCh38 Supplementary_files_format_and_content: Text file containing RNA-Seq read counts per gene for all samples claculated with STAR 2.5.3a.
|
|
|
Submission date |
Jul 04, 2020 |
Last update date |
Jul 05, 2020 |
Contact name |
Monta Brīvība |
E-mail(s) |
monta@biomed.lu.lv
|
Organization name |
Latvian Biomedical Research and Study Centre
|
Street address |
Ratsupites 1
|
City |
Riga |
ZIP/Postal code |
LV-1067 |
Country |
Latvia |
|
|
Platform ID |
GPL17303 |
Series (1) |
GSE153792 |
Whole-blood transcriptome profiling reveals signatures of metformin and its therapeutic response |
|
Relations |
BioSample |
SAMN15447736 |
SRA |
SRX8666573 |