|
| Status |
Public on Feb 20, 2014 |
| Title |
fXPC 6 |
| Sample type |
RNA |
| |
|
| Source name |
Peripheral blood
|
| Organism |
Homo sapiens |
| Characteristics |
age of punction: 58
age of onset: 62
gender: Male
clinical signs: 2 major
adiological signs: 1major + 1minor
|
| Extracted molecule |
total RNA |
| Extraction protocol |
2,5ml of peripheral blood was extracted from patients. PAXgene Blood RNA Kit was used to isolte total RNA according to the manufacturer's instructions
|
| Label |
Cy3
|
| Label protocol |
Cyanine-3 (Cy3) labeled cRNA was prepared from 100ng of total RNA using the LowInputQuick Amp Labeling kit – Agilent 5190-2305 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 |
600 ng of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Human Gene Expression 8x60K microarray (amadid id: 28004) 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)
|
| Scan protocol |
Scanned on an Agilent G2539A scanner at 3um resolution and 100%PMT. The intensity data of each individual hybridization were extracted and the quality was assessed with the Feature Extraction software 10.7 (Agilent).
|
| Data processing |
Raw data was corrected for background noise using the normexp method. Quantile normalization was applied to assure comparability across samples.
|
| |
|
| Submission date |
Jul 15, 2013 |
| Last update date |
Feb 20, 2014 |
| Contact name |
Elisabet Mateu Huertas |
| E-mail(s) |
elisabet.mateu@crg.es
|
| Organization name |
Center for Genomic Regulation
|
| Department |
Bioinformatics and Genomics
|
| Lab |
Xavier Estivill
|
| Street address |
Dr. Aiguader, 88
|
| City |
Barcelona |
| State/province |
Barcelona |
| ZIP/Postal code |
08003 |
| Country |
Spain |
| |
|
| Platform ID |
GPL13607 |
| Series (2) |
| GSE48873 |
Blood expression profiles of fragile X premutation carriers identify genes involved in neurodegenerative and infertility phenotypes [FXTAS] |
| GSE48903 |
Blood expression profiles of fragile X premutation carriers identify genes involved in neurodegenerative and infertility phenotypes |
|
