|
| Status |
Public on Nov 19, 2020 |
| Title |
FH_positive_sample_18 |
| Sample type |
RNA |
| |
|
| Source name |
Before exercise
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Vastus lateralis muscle
family history of type 2 diabetes: Yes
gender: Male
|
| Treatment protocol |
Muscle biopsies were taken from the right vastus lateralis muscle under local anesthesia (Lidocaine 1%), using a 6 mm Bergström needle (Stille AB, Sweden). Biopsies were immediately stored in RNAlater (Ambion, Austin, TX) and after overnight incubation at 4 C snap frozen at -80 C until further processing. The double staining method was used for capillary staining. Myofibrillar ATPase histochemistry was performed by preincubation at pH 4.4, 4.6, and 10.3 to identify muscle fiber types. Computer image analysis was performed using BioPix IQ 2.0.16 software (BioPix AB, Sweden)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using Tri reagent (Sigma-Aldrich, St. Louis, MO) followed by RNeasy Midi kit (Qiagen, Düsseldorf, Germany). The RNA was further concentrated by RNeasy MiniElute (Qiagen, Düsseldorf, Germany) and SpeedVac (DNA 120 SpeedVac, Thermo Savant, Waltham, MA)
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to the standard Affymetrix protocol from total RNA (Expression Analysis Technical Manual, Affymetrix)
|
| |
|
| Hybridization protocol |
Hybridization to the Affymetrix Custom Array NuGO-Hs1a520180 GeneChip (http://www.nugo.org) were performed according to the manufacturer’s recommendation
|
| Scan protocol |
Images were analyzed using the GeneChip Operating System (GCOS; Affymetrix) software
|
| Description |
Gene expression data before exercise
|
| Data processing |
We used ENTREZ custom chip definition files (http://brainarray.mbni.med.umich.edu) to regroup the individual probes into consistent probesets and remap to the correct sets of genes for Affymetrix Custom Array NuGO-Hs1a520180 array which resulted in a total of 16,313 genes. We used the GC-content robust multi-array average (GC-RMA) method with additional background adjustment using sequence information to estimate probe affinity for nonspecific binding, quantile-based normalization, and summarization based on a multi-array model fit using the median polish algorithm
|
| |
|
| Submission date |
Nov 18, 2020 |
| Last update date |
Nov 19, 2020 |
| Contact name |
Hemang Mahendrakumar Parikh |
| Organization name |
University of South Florida
|
| Department |
Health Informatics Institute
|
| Street address |
3650 Spectrum Blvd.
|
| City |
Tampa |
| State/province |
FL |
| ZIP/Postal code |
33612 |
| Country |
USA |
| |
|
| Platform ID |
GPL7144 |
| Series (2) |
| GSE161719 |
Relationship between insulin sensitivity and gene expression in human skeletal muscle (Study A) |
| GSE161721 |
Relationship between insulin sensitivity and gene expression in human skeletal muscle |
|
