|
| Status |
Public on Nov 15, 2011 |
| Title |
ZnD-10d_PAX_pooled |
| Sample type |
RNA |
| |
|
| Source name |
Human peripheral blood, zinc depleted, 10 d
|
| Organism |
Homo sapiens |
| Characteristics |
gender: Male
age: Adult
treatment: Zinc-Depleted for 10 d
tissue: Whole blood
sampling method: PAXgene system
rna subtype: Total RNA
|
| Treatment protocol |
In order to establish a defined baseline condition prior to dietary zinc depletion, subjects consumed meals composed of a mixed diet providing ~11 mg Zn/d for 7 d. An egg white-based liquid formula which provided <0.5 mg Zn/d was consumed during the following 10 d for acute dietary zinc depletion.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from whole blood collected in PAXgene tubes (BD) was extracted using the Qiagen Rneasy kit according to manufactuer's instructions. Globin RNA contents in the isolated whole blood RNA was reduced by the GLOBINclear kit (Ambion). Purity and integrity of yielded RNA were assessed with the NanoDrop spectrophotometer and Agilent Bioanalyzer, respectively.
|
| Label |
Biotin
|
| Label protocol |
Biotinylated cRNA were prepared with the Illumina TotalPrep RNA Amplification kit (Ambion)
|
| |
|
| Hybridization protocol |
Standard Illumina hybridization protocol
|
| Scan protocol |
Standard Illumina scanning protocol
|
| Description |
Pooled
|
| Data processing |
Probes with detection P-values above 0.05 in all samples were excluded from the dataset by the Illumina GenomeStudio software. Absolute signal intensities of the filtered probes were quantile normalized using EXPANDER 5.2 (Ulitsky I et al. 2010, Nat Protoc. 2010;5:303-22).
|
| |
|
| Submission date |
Oct 24, 2011 |
| Last update date |
May 17, 2012 |
| Contact name |
Robert J. Cousins |
| E-mail(s) |
cousins@ufl.edu
|
| Organization name |
University of Florida
|
| Department |
Food Science and Human Nutrition Department, Center for Nutritional Sciences
|
| Lab |
Nutritional Genomics Laboratory
|
| Street address |
359 FSHN Bldg. Newell Dr. PO Box 110370
|
| City |
Gainesville |
| State/province |
Florida |
| ZIP/Postal code |
32611-0370 |
| Country |
USA |
| |
|
| Platform ID |
GPL10558 |
| Series (1) |
| GSE33174 |
Effects of acute dietary zinc depletion on the gene expression profile of whole blood in human male adults |
|
