10 protocols
AccessionNameType
P-GSE49851-1
normalization data transformation protocol
R/Bioconductor RMA algorithm implemented in oligo package ver 1.22.0 ID_REF = VALUE = log2 RMA signal
P-GSE49851-7
array scanning protocol
Affymetrix GeneAtlas System
P-GSE49851-6
hybridization protocol
Affymetrix guidelines for GeneAtlas instrument
P-GSE49851-2
normalization data transformation protocol
The quantified signals were background corrected (Normexp with offset value 10, see Ritchie et al. 2007) and normalized using quantile normalization method. [Service conducted at Exiqon Services, Denmark.] ID_REF = VALUE = log2 quantile normalized signal intensity Hy3
P-GSE49851-10
array scanning protocol
The microarray slides were scanned and stored in an ozone free environment (ozone level below 2.0 ppb) in order to prevent potential bleaching of the fluorescent dyes. The miRCURY LNATM microRNA Array slides were scanned using the Agilent G2565BA Microarray Scanner System (Agilent Technologies, Inc., USA) and the image analysis was carried out using the ImaGene 9.0 software (BioDiscovery, Inc., USA). [Service conducted at Exiqon Services, Denmark.]
P-GSE49851-9
hybridization protocol
The hybridization was performed according to the miRCURY LNATM microRNA Array Instruction manual using a Tecan HS4800TM hybridization station (Tecan, Austria). [Service conducted at Exiqon Services, Denmark.]
P-GSE49851-8
labelling protocol
750 ng total RNA from sample was labeled with Hy3TM fluorescent label, using the miRCURY LNATM microRNA Hi-Power Labeling Kit, Hy3TM/Hy5TM (Exiqon, Denmark) following the procedure described by the manufacturer. The Hy3TM-labeled samples were hybridized to the miRCURY LNATM microRNA Array 7'th (Exiqon, Denmark), which contains capture probes targeting all microRNAs for human, mouse or rat registered in the miRBASE 18.0. [Service conducted at Exiqon Services, Denmark.]
P-GSE49851-3
sample treatment protocol
Amygdala electrical stimulation model of temporal lobe epilepsy.
P-GSE49851-4
nucleic acid extraction protocol
Total RNA including miRNA was isolated from the left dentate gyrus region from hippocampi isolated on ice and placed in RNAlater solution (Ambion, AM7024) and stored at -20C until use. Isolation from dissected left dentate gyrus was performed by miRNease Mini kit (QIAGEN, 217004), according to the manufacturer's instructions.
P-GSE49851-5
labelling protocol
100 ng of total mRNA was used for cDNA synthesis using Ambion WT Expression Kit (Life Technologies #4411974).