|
| Status |
Public on Feb 20, 2014 |
| Title |
V79 Exp F |
| Sample type |
RNA |
| |
|
| Source name |
Neuroblastoma cell line SH-SY5Y_V79
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: Neuroblastoma cell line SH-SY5Y
transfection: pCAGIG expressing the mutant 5'UTR of the FMR1 gene (79 CGG repeats)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA extraction was carreid out using miRNeasy (Qiagen) following manufacturer’s instructions.
|
| Label |
Cy3
|
| Label protocol |
Cyanine-3 (Cy3) labeled cRNA was prepared from 100ng 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 |
600ng 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 25 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 arrays (G4851A-028004) 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).
|
| Description |
SH-SY5Y cells were transfects with a pCAGIG expressing the mutant 5'UTR of the FMR1 gene (79 CGG repeats). Total RNA was isolated 24 h after transfection using miRNeasy (Qiagen) following manufacturer’s instructions.
IntNorm_Cy3_F.V80_1_3
|
| 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 16, 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 |
GPL16699 |
| Series (2) |
| GSE48902 |
Blood expression profiles of fragile X premutation carriers identify genes involved in neurodegenerative and infertility phenotypes [SHSY5Y] |
| GSE48903 |
Blood expression profiles of fragile X premutation carriers identify genes involved in neurodegenerative and infertility phenotypes |
|
