Whole genome transcriptome data from the retrosplenial cortex and hippocampus of female and male control and APP/PS1 Alzheimer’s disease mice.

Description

The uploaded transcriptome data were obtained from APPswePS1dE9 transgenic mice with a C57BL/6J background (APPPS1) and related control animals. The APPPS1 Alzheimer mouse line carries a human APP with Swedish double mutation (APPswe) cointegrated with human PS1 with exon 9 deletion (PS1dE). The mutant mice (B6.Cg-Tg(APPswe, PSEN1dE9)85Dbo/Mmjax, MMRRC stock no. 34832-JAX) and their wildtype littermates were purchased from Jackson Laboratory. In total, eight control animals (four ♂, age: 32.72 ± 0.38 weeks; four ♀, age: 32.14 ± 0.25 weeks) and eight APPswePS1dE mice (three ♂, age: 32.81 ± 0.24 weeks; five ♀, age: 32.66 ± 0.39 weeks) were used for hippocampal and cortical extirpation and subsequent transcriptome analysis. Importantly, both sexes were used and analyzed. Note that the experimental animals were labeled in the dataset as follows: Four male control mice: Control #1, Control #2, Control #3, Control #4 (note that for Control #4 no transcriptome data from the RS cortex were obtained) Four female control mice: Control #5, Control #6, Control #7, Control #8 Three male APPPS1 mice: APPPS1 #1, APPPS1 #2, APPPS1 #3 Five male APPPS1 mice: APPPS1 #4, APPPS1 #5, APPPS1 #6, APPPS1 #7, APPPS1 #8 (note that for APP/PS1 #8 no transcriptome data from the hippocampus were obtained) All experimental mice were housed in groups of 3-4 in clear Makrolon cages type II with ad libitum access to drinking water and standard food pellets. Mice were maintained at an ambient temperature of 21 ± 2°C, 50–60% relative humidity, and on a conventional 12 h/12 h light/dark cycle beginning at 5:00 am using ventilated cabinets (Model 9AV125P, (Tecniplast, Germany). All animals were strictly adapted to the circadian pattern preceding subsequent cortical and hippocampal extirpation and RNA isolation.

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Retrosplenial (RS) cortex and hippocampus preparation and tissue storage: Experimental animals were deeply anaesthetized using ketamine (100 mg/kg) / xylazine (10 mg/kg) i.p. Animals were decapitated, the brain was immediately removed and placed in a clean RNase-free petri-dish filled with pure RNAlater reagent (Qiagen, Germany). By using a scalpel, forceps and a brush the whole hippocampus and a piece (2-3 mm3) of the retrosplenial cortex was dissected from both brain hemispheres. Each tissue fragment was placed in a 2 ml reaction tube, snap frozen in liquid nitrogen and stored at -80°C until RNA preparation. Cortical and hippocampal RNA isolation: Total RNA was isolated using Lipid Tissue Mini Kit (Qiagen, Germany) according to the manufacturer’s instructions (incl. optional DNase digestion step). Tubes including the dissected cortical and hippocampal tissue were removed from -80°C, immediately lysed in Qiazol lysis buffer and homogenized using the Tissue Ruptor (Qiagen, Germany). Following phenol-chloroform separation, DNase digestion and washing steps, total RNA was eluted in 30 µl RNase-free ddH20. The quantity and quality of the eluted RNA was checked using Nanodrop 1000 (ThermoScientific, USA) and a quality check was carried out before RNA hybridization to microarrays chips using the BioAnalyzer 2100 (Agilent Technology, USA). One-Color Microarray-Based Gene Expression Analysis: The One-Color Microarray-Based Gene Expression system by Agilent Technologies utilizes the Low Input Quick Amp Labeling Kit to generate cDNA (1st and 2nd strand cDNA). Samples are labeled with a T7 RNA polymerase blend. This polymerase incorporates Cyanine 3-CTP during amplification generating an one-color fluorescent complimentary RNA (cRNA) as target material. The labeled/amplified cRNA is purified using the RNeasy Mini Kit (Qiagen GmbH, Germany) followed by quantification of the cRNA using the NanoDrop. After finalization of cRNA sample preparation, hybridization of samples is carried out for 17 hrs (65°C) using the Gene Expression Hybridization Kit (Agilent Technologies Germany GmbH & Co. KG, Germany) and the SurePrint G3 Mouse Gene Expression v2 8x60K Microarray Kit (Agilent Technologies Germany GmbH & Co. KG, Germany) according to the manufacturer's instructions (Table 2). After the washing procedure with Gene Expression Wash Buffer Kit (Agilent Technologies Germany GmbH & Co. KG, Germany) to remove unspecific bindings, the microarrays are prepared for scanning and feature extraction. The microarray scan was performed using the Agilent SureScan Microarray Scanner (Agilent Technologies Germany GmbH & Co. KG, Germany). Feature Extraction Software (Agilent Technologies Germany GmbH & Co. KG, Germany) was used to extract the information from the probe features of the microarray scan data, providing information about gene expression/transcripts for further analysis. For further information please refer to our related publication in Data in Brief.

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