|
| Status |
Public on Mar 31, 2014 |
| Title |
hippocampus_CA3_febrile seizure FS5 |
| Sample type |
RNA |
| |
|
| Source name |
hippocampus, CA3
|
| Organism |
Homo sapiens |
| Characteristics |
gender: Female
febrile seizure: yes
age of ipi (yr/mo): 2yr
age of epilepsy onset (yr): 14
age of epilepsy duration (yr): 5
age at surgery: 19yr
side: right
|
| Treatment protocol |
Fresh ex-vivo explants of patients were obtained at the surgery room and immediately preserved with 600 uL of RNAlater (Qiagen).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Brain tissue explants from GD (3-4 mm3) were homogenized with TissueRupter (Qiagen) and total RNA was extracted from the homogenates using the RNeasy Lipid Tissue Kit (Qiagen)
|
| Label |
Cy3
|
| Label protocol |
Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Microarray-Based Gene Expression Analysis - Quick Amp Labeling (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (Qiagen). RNA concentration and purity was determined by reading the absorbance at 260 and 280 nm on a spectrophotometer (NanoVue, GE Health Care, USA).
|
| |
|
| Hybridization protocol |
1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112F) for 17 hours at 65°C in a rotating Agilent hybridization oven. 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112F) for 17 hours at 65°C in a rotating Agilent hybridization oven.
|
| Scan protocol |
Slides were scanned immediately after washing on the Agilent Bundle using one color scan setting for 1x44k array slides.
|
| Description |
Gene expression from CA3 explant
|
| Data processing |
The scanned images were analyzed with Feature Extraction Software version 9.5.3.1 (Agilent) using default parameters (protocol GE1-v5_95 and Grid: 014850_D__F_20060807) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.
|
| |
|
| Submission date |
Apr 17, 2011 |
| Last update date |
Mar 31, 2014 |
| Contact name |
Carlos Alberto Moreira-Filho |
| E-mail(s) |
carlos.moreira@hc.fm.usp.br
|
| Phone |
55-11-3061-8449
|
| Organization name |
Faculdade de Medicina da Universidade de Sao Paulo
|
| Department |
Departments of Pediatrics
|
| Lab |
LIM36
|
| Street address |
Av. Dr. Eneas Carvalho de Aguiar 647
|
| City |
Sao Paulo |
| State/province |
SP |
| ZIP/Postal code |
05403-900 |
| Country |
Brazil |
| |
|
| Platform ID |
GPL6480 |
| Series (1) |
| GSE28674 |
Hippocampal CA3 Transcriptome Signature and Dentate Gyrus MRI Features Correlate with Initial Precipitating Injury in Refractory Temporal Lobe Epilepsy |
|
