|
| Status |
Public on Nov 19, 2020 |
| Title |
Before_Basal_sample_4 |
| Sample type |
RNA |
| |
|
| Source name |
Before bed rest
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Vastus lateralis muscle
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 |
Cy3
|
| Label protocol |
Cyanine-3 (Cy3) labeled cRNA was prepared from RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions
|
| |
|
| Hybridization protocol |
Targets were hybridized to the one-color Cyanine-3 (Cy3, green) Agilent Whole Human Genome Oligo Microarray (G4112F (Feature Number version)) which contains 44,000 60-mer oligonucleotide probes representing 41,000 unique genes and transcripts. Probe labeling and hybridization were performed according to manufacturer’s recommendation
|
| Scan protocol |
Images were analyzed using the Agilent Feature Extraction Software (version 9.5)
|
| Description |
Gene expression before bed rest
|
| Data processing |
The median intensities of each spot on the array were calculated using the GenePix Pro software (version 6). We performed quantile-based normalization between arrays without background subtraction using linear models for microarray data (limma) package in R
|
| |
|
| 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 |
GPL4133 |
| Series (2) |
| GSE161720 |
Relationship between insulin sensitivity and gene expression in human skeletal muscle (Study B) |
| GSE161721 |
Relationship between insulin sensitivity and gene expression in human skeletal muscle |
|
