characteristics.text: ERC000011
characteristics.characteristic: ENA-CHECKLIST
characteristics.text: 2023-10-13T08:38:16Z
characteristics.characteristic: ENA-FIRST-PUBLIC
characteristics.text: 2023-10-13T08:38:16Z
characteristics.characteristic: ENA-LAST-UPDATE
characteristics.text: SAMEA112648563
characteristics.characteristic: External Id
characteristics.text: UCB Biopharma SRL
characteristics.characteristic: INSDC center name
characteristics.text: 2023-10-13T08:38:16Z
characteristics.characteristic: INSDC first public
characteristics.text: 2023-10-13T08:38:16Z
characteristics.characteristic: INSDC last update
characteristics.text: public
characteristics.characteristic: INSDC status
characteristics.text: ERS14646283
characteristics.characteristic: SRA accession
characteristics.text: E-MTAB-12634:UCB-049
characteristics.characteristic: Submitter Id
characteristics.text: 469
characteristics.unit: day
characteristics.characteristic: age
characteristics.text: ArrayExpress
characteristics.characteristic: broker name
characteristics.text: house mouse
characteristics.characteristic: common name
characteristics.text: Protocols: Unilateral, intrahippocampal kainic acid (ihKA) or NaCl injections were performed in adult male USP15fl/fl Cre/+ mice and USP15fl/fl littermates. Mice were anesthetized and received analgesic treatment (100 mg/kg ketamine, 5 mg/kg xylazine, 0.1 mg/kg atropine, i.p. and 4 mg/kg carprofen, s.c) and placed into a stereotaxic frame (David Kopf Instruments, CA, USA) in flat skull position. KA solution (50nl, 20 mM in 0,9% sterile NaCl, Tocris) was injected into the right dorsal hippocampus (coordinates from bregma (in mm): anterioposterior (AP) = -2.0, mediolateral (ML) = -1.4, dorsoventral (DV) = -1.9) with a metal cannula (Harry Rieck Edelstahl) connected to a Hamilton syringe (Hamilton Bonaduz AG) and a micropump. Controls received NaCl solution only. After injection, mice were transferred to their home cage and kept under video surveillance for at least 8h (mean 18.1h, range 8-23h). Seven days later, mice were implanted with electrodes (anesthesia see above, additional 0.1 mg/kg buprenorphine). Custom-made platinum-iridium wire electrodes (Ø125 µm, Teflon-insulated, WPI) were implanted in both hippocampi (coordinates from bregma in mm: AP -2.0, ML -1.4/+1.4, DV -1.9) and two jeweler’s screws in the skull anterior to bregma served as ground and reference. Wires were soldered to a connector permanently mounted on the skull with cyanoacrylate and dental cement. Mice received buprenorphine and carprofen analgesia for the days after surgery. At day 18 after KA injection, tamoxifen treatment was applied for 5 days (day 21-25; Sigma-Aldrich, 0.15ml of a 10mg/ml solution in corn oil) to delete Usp15 expression. Perfusion was performed at day 46. Mice were anesthetized with ketamine (100 mg/kg) and medetomidine (Dormitor; 1 mg/kg) and transcardial perfusion was performed with 30 ml phosphate buffered saline (PBS, ph 7.4). Brains were excised immediately afterwards and both hippocampi were prepared in ice-cold PBS, snap frozen in individual RNAse-free, sterile tubes in liquid nitrogen and stored at -80°C until all samples were collected. Total RNA was extracted from both left and right mouse hippocampi using RNeasy Plus Mini Kit (Qiagen, 74134) following manufacturer’s instructions. RNA concentration was measured with a NanoDrop ND-1000 Spectrophotometer. RNA quality was assessed using the Bio-Rad Experion Automated Electrophoresis System (RQI ≥ 7.3). The NEBNext Ultra II Directional RNA Library Prep Kit for Illumina was used to process the sample(s). The sample preparation was performed according to the protocol \"NEBNext Ultra II Directional RNA Library Prep Kit for Illumina\" (NEB #E7760S/L). Briefly, mRNA was isolated from total RNA using the oligo-dT magnetic beads. After fragmentation of the mRNA, a cDNA synthesis was performed. This was used for ligation with the sequencing adapters and PCR amplicification of the resulting product. The quality and yield after sample preparation was measured with the Fragment Analyzer (see appendices). The size of the resulting products was consistent with the expected size distribution (a broad peak between 300-500 bp).
characteristics.characteristic: description
characteristics.text: adult
characteristics.characteristic: developmental stage
characteristics.text: USP15fl/fl
characteristics.characteristic: genotype
characteristics.text: 86
characteristics.characteristic: individual
characteristics.text: not applicable
characteristics.characteristic: isolate
characteristics.text: Mus musculus
characteristics.characteristic: organism
characteristics.text: Mus musculus
characteristics.characteristic: organism
characteristics.text: hippocampal formation
characteristics.characteristic: organism part
characteristics.text: wild type phenotype
characteristics.characteristic: phenotype
characteristics.text: right hippocampal formation
characteristics.characteristic: sampling site
characteristics.text: Mus musculus
characteristics.characteristic: scientific_name
characteristics.text: male
characteristics.characteristic: sex
characteristics.text: C57Bl/6J
characteristics.characteristic: strain
characteristics.text: UCB-049
characteristics.characteristic: title