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Sample GSM4654162 Query DataSets for GSM4654162
Status Public on Jul 05, 2020
Title 8_2
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: after three months long metformin course
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 SAMN15447713
SRA SRX8666562

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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