|
| Status |
Public on May 15, 2015 |
| Title |
Control_9 |
| Sample type |
RNA |
| |
|
| Source name |
Human blood, Control
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: whole blood
gender: male
age: 45
|
| Treatment protocol |
The mRNA profiling in human blood samples (IRB #AS 14039) divided into three groups: control (unexposed workers; n = 12), short-term exposure (workers exposed to VOCs for less than 10 years; n = 12), and long-term exposure (workers exposed to VOCs for more than 10 years; n = 12) were used after exposure to VOCs
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total mRNA was prepared using the PAXgene miRNA Kit (Qiagen, Valencia, CA, USA) following the manufacturer's recommendations. RNA yields were assessed using a NanoDrop (Thermo Fisher Scientific, USA), and the qualities of RNA were confirmed using a 2100 Bioanalyzer (Agilent Technologies, CA, USA).
|
| Label |
Cy3
|
| Label protocol |
Cyanine-3 (Cy3) labeled cRNA was prepared from total RNA(200ng) using the One-Color Low RNA Input Linear Amplification kit (Agilent) according to the manufacturer's instructions. Dye incorporation and cRNA yield were checked with the NanoDrop (Thermo Fisher Scientific, USA).
|
| |
|
| Hybridization protocol |
600ng of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 10x Gene Expression blocking agent and 25x Agilent fragmentation buffer following the manufacturers’ instructions. On completion of the fragmentation reaction, 25 ul of 2x Hi-RPM Hybridization Buffer was added to the fragmentation mixture and hybridized to Agilent Human GE 8x 60K (ver.2) oligo arrays (Agilent Technologies) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.
|
| Scan protocol |
Slides were scanned immediately after washing on the Agilent C scanner (Agilent Technologies) using one color scan setting Human GE 8x 60K (ver.2) oligo arrays slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green PMI and the gain of PMI is set to 100%).
|
| Description |
Gene expression of control_9
|
| Data processing |
The scanned images were analyzed Feature Extraction software 10.7.3.1 (Agilent Technologies) and the extracted raw data were analyzed by GeneSpring GX v13.0 (Agilent Technologies). Gene expression data were flaged and normalized for 23070 probes of 50599 probes by quantile normalization. We used unpaired t-tests for selection of commonly expressed and differentially expressed genes. Genes were judged if P-values were 0.05 or less and fold changes were at least 1.5 compared with gene expression in the control group.
|
| |
|
| Submission date |
May 14, 2015 |
| Last update date |
May 15, 2015 |
| Contact name |
jiyoung hong |
| E-mail(s) |
skydaniel3@naver.com
|
| Phone |
82-10-8992-9924
|
| Organization name |
hanyang university
|
| Street address |
Hanyang Univ.,55, Hanyangdaehak-ro, Sangrok-Gu
|
| City |
Ansan |
| ZIP/Postal code |
426-791 |
| Country |
South Korea |
| |
|
| Platform ID |
GPL17077 |
| Series (2) |
| GSE68906 |
Identification of time-dependent biomarkers and effects of exposure to volatile organic compounds using high-throughput analysis (expression) |
| GSE68909 |
Identification of time-dependent biomarkers and effects of exposure to volatile organic compounds using high-throughput analysis |
|
