|
| Status |
Public on Aug 28, 2012 |
| Title |
Human in vivo, environmental exposure, subject 5 |
| Sample type |
RNA |
| |
|
| Source name |
Human PMBC_environmental exposure nickel
|
| Organism |
Homo sapiens |
| Characteristics |
subject group: reference
exposure to nickel: environmental
tissue: blood
cell type: peripheral blood mononuclear cells
batch: 1
|
| Extracted molecule |
total RNA |
| Extraction protocol |
50 mL of blood was collected from each subject by venipuncture by a local registered nurse. PBMC were isolated from blood using a standard Ficoll-Gradient procedure. PBMCs were frozen Trizol at -80C. Total RNA was extracted from each sample according to the TRIzol (Invitrogen) manufacturer's protocol
|
| Label |
biotin
|
| Label protocol |
cRNA probes were synthesized and labeled using GeneChip Whole Transcript Terminal Labeling Expression Kit (Affymetrix).
|
| |
|
| Hybridization protocol |
Samples were hybridized to a GeneChip Human Gene 1.0 ST Array (Affymetrix) that contains 28,869 well annotated genes.
|
| Scan protocol |
Hybridization and scanning of the arrays was performed using a standard procedure
|
| Description |
E5
|
| Data processing |
Gene expression analyses were performed using R. Gene expression data were imported and normalized in batches using the Affymetrix package and robust multichip average (RMA) [Affy package v.1.30.0. in R v.2.13.2 GUI 1.42 Leopard build 32-bit]. Samples were then batch normalized and log-transformed using an empirical Bayes approach with the R package COMBAT [VA 3.0.2 in R 2.14.0 GUI 1.42 Leopard build 32-bit]. Significance of gene expression changes between the exposed and referent populations was assessed using a gene-wise linear model approach with LIMMA, which utilizes an empirical Bayes approach to generate moderated t-statistics by taking into account the standard errors and estimated log-fold changes.
|
| |
|
| Submission date |
Aug 27, 2012 |
| Last update date |
Aug 28, 2012 |
| Contact name |
Adriana Arita |
| E-mail(s) |
[email protected]
|
| Phone |
646-361-8166
|
| Organization name |
New York University
|
| Street address |
57 Old Forge Road
|
| City |
Tuxedo |
| ZIP/Postal code |
10987 |
| Country |
USA |
| |
|
| Platform ID |
GPL6244 |
| Series (1) |
| GSE40392 |
Gene expression of PBMC of chinese nickel refinery workers when compared to the gene expression profile of PBMCs from referent subjects |
|
