|
| Status |
Public on Aug 14, 2019 |
| Title |
BAR-TR38_T0 |
| Sample type |
RNA |
| |
|
| Source name |
vastus lateralis
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Skeletal muscle
group: Obese
time point: Before metabolic surgery
|
| Treatment protocol |
No treatment RNA extracted from frozen tissu
|
| Extracted molecule |
total RNA |
| Extraction protocol |
total RNA extracted following the manufacturer's recommendations, miRNA micro kit ( Qiagen, Hilden, Germany), The protocol includes separation of organic and aqueous layers, and an on-column DNase digestion
|
| Label |
Cy3
|
| Label protocol |
Cy3-labeled cRNA. For labelling, the Low Input QuickAmp Labeling Kit (Agilent Technologies) is used to generate fluorescent cRNA (complementary RNA). For 1st strand synthesis, either oligo-dT primer or a random primer / oligo-dT primer mixture (WT primer) is used. After 2nd strand synthesis, an in vitro transcription for synthesis of cRNA labelled with cyanine 3-CTP is performed. Please refer the summary file for details regarding the used primer, yield of cRNA as well as cy3 incorporation rate
|
| |
|
| Hybridization protocol |
For each cRNA is hybridised on 8x60K microarrays at 65 ◦C for 17 h using Agilent’s recommended hybridisation chamber and oven. Afterwards microarrays are washed once with the Agilent Gene Expression Wash Buffer 1 for one minute at ambient temperature followed by a second wash with preheated (37 ◦C) Gene Expression Wash Buffer 2 for one minute.
|
| Scan protocol |
Fluorescence signals on microarrays are detected by the SureScan Microarray Scanner (Agilent Technologies) at a resolution of 3 micron for SurePrint G3 Gene Expression Microarrays and 5 micron for HD Microarray formats, generating a 20 bit TIFF file.FSlides were scanned using one color scan setting for 4x44k array slides.
|
| Description |
Gene expression of lean controls
|
| Data processing |
The scanned images were analyzed with Feature Extraction Software 11 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. Data was filtered using 0.1 quantile cutoff to eliminate low level signals.
|
| |
|
| Submission date |
Jul 26, 2019 |
| Last update date |
Aug 15, 2019 |
| Contact name |
Annette Schürmann |
| E-mail(s) |
schuermann@dife.de
|
| Organization name |
German Institute of Human Nutrition Potsdam-Rehbruecke
|
| Department |
Department of Experimental Diabetology
|
| Street address |
Arthur-Scheunert-Allee 114-116
|
| City |
Nuthetal |
| State/province |
BRB |
| ZIP/Postal code |
14558 |
| Country |
Germany |
| |
|
| Platform ID |
GPL26966 |
| Series (2) |
| GSE134956 |
Dynamic changes of muscle insulin sensitivity after metabolic surgery II |
| GSE135066 |
Dynamic changes of muscle insulin sensitivity after metabolic surgery |
|
