|
| Status |
Public on Dec 05, 2014 |
| Title |
Blood_control 11 [NC90] |
| Sample type |
RNA |
| |
|
| Source name |
healthy control
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: peripheral blood mononuclear cells
|
| Treatment protocol |
Integrity and concentration of RNA were assessed after RNA extraction and prior to sample labeling.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from each sample was quantified by the NanoDrop ND-1000 and RNA integrity was assessed by standard denaturing agarose gel electrophoresis.
|
| Label |
cy3
|
| Label protocol |
Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.
|
| |
|
| Hybridization protocol |
1 μg of each labeled cRNA was fragmented by adding 11 μl 10 × Blocking Agent and 2.2 μl of 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 55 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 100 μl of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.
|
| Scan protocol |
The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505C).
|
| Description |
Healthy controls < 18 years
|
| Data processing |
Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v11.5.1 software package (Agilent Technologies). After quantile normalization of the raw data, LncRNAs and mRNAs that at least 20 out of 30 samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis.
note from submitter: The raw file is the most original data received from the company, containing ~17000 probes.
|
| |
|
| Submission date |
Feb 12, 2014 |
| Last update date |
Dec 05, 2014 |
| Contact name |
Fuquan Zhang |
| E-mail(s) |
zfq99@hotmail.com
|
| Organization name |
Wuxi mental health center
|
| Street address |
156 Qianrong Rd
|
| City |
Wuxi |
| ZIP/Postal code |
214151 |
| Country |
China |
| |
|
| Platform ID |
GPL15314 |
| Series (2) |
| GSE54913 |
mRNA expression in blood of 18 schizophrenia patients and 12 healthy controls |
| GSE54914 |
Expression in blood of schizophrenia patients and healthy controls |
|
