|
| Status |
Public on Jun 01, 2015 |
| Title |
Human in vivo, low arsenic exposure, male 2 |
| Sample type |
RNA |
| |
|
| Source name |
Human PMBC Environmental
|
| Organism |
Homo sapiens |
| Characteristics |
gender: male
cell type: PBMC
exposure: Low Arsenic Drinking Water
batch: 2
|
| Treatment protocol |
At the time of enrollment, study participants had been exposed to water arsenic (wAs) between 50 and 1000 µg/L and were given a water filtration system for removal of As
|
| Growth protocol |
Blood and urine collection, sample handling, and PBMC isolation for this study were performed as previously described (Chervona et al., 2012). Briefly, blood samples were obtained by venipuncture, and collected into EDTA-containing vacutainer tubes, which were then placed in IsoRack/IsoPack cool packs (Brinkmann Instruments). Samples were transported in hand-carried coolers to the local laboratory at the field clinic in Araihazar, within four hours of collection. Samples were centrifuged for 10 minutes at 3,000 × g at 4°C, and the plasma fraction was stored at −80°C. PBS was added to the remaining cells followed by a ficoll-hypaque gradient extraction of PBMCs using standard techniques. PBMCs were stored at −80°C
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using Trizol (Invitrogen). The isolated T.RNA was subjected to a colum purification using Rneasy Plus Micro Kit (Qiagen)
|
| Label |
biotin
|
| Label protocol |
Sense strand cDNA probes were synthesized (amplified) using Ambion Whole Transcript Expression Kit. Amplified single stranded c.DNA was fragmented and labeled using GeneChip WT Terminal Labeling Kit (Affymetrix)
|
| |
|
| Hybridization protocol |
The fragmented and labeled DNA underwent hybridization with Affymetrix GeneChip Human Gene 1.0 ST Array at the NYU Cancer Insitute Genomics Facility.
|
| Scan protocol |
Array scanning was performed according to the manufacturer's instruction (Affymetrix)
|
| Data processing |
Gene expression analyses were performed using R. Gene expression data were imported and normalized using a single-sample method, single channel array normalization (Piccolo et al. 2012) in R 2.15.0 GUI 1.53 64-bit. SCAN normalization performs probe summarization as part of normalization procedure and utilizes the custom CDF provided by Brainarray to do so. Data was further processed to expression sets using the Affymetrix package version 1.30.0. in R 2.15.1 GUI 1.42 Leopard build 64-bit.
HuGene10stv1_Hs_ENTREZG_15.1.0 http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/15.1.0/entrezg.asp
HuGene10stv1_Hs_ENTREZG_15.1.0 http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/15.1.0/entrezg.asp
|
| |
|
| Submission date |
May 15, 2014 |
| Last update date |
Jun 01, 2015 |
| Contact name |
Alexandra Brooke Munoz |
| E-mail(s) |
abm362@nyu.edu
|
| Organization name |
NYU Medical Center
|
| Department |
Environmental Medicine
|
| Lab |
Costa Lab
|
| Street address |
57 Old Forge Road
|
| City |
Tuxedo |
| State/province |
New York |
| ZIP/Postal code |
10987 |
| Country |
USA |
| |
|
| Platform ID |
GPL16522 |
| Series (1) |
| GSE57711 |
Sex-related changes in gene expression patterns of adults exposed to arsenic contaminated drinking water |
|
