GSM4649193: Midbrain control rep3; Danio rerio; RNA-Seq
A total of 18 fish (9 hypoxic and 9 normoxic) were sacrificed after anesthetizing with 0.03% tricaine (Sigma-Aldrich, Germany), and brains were separated and placed in ice-cold HBSS (1X Hank's basal salt solution, 2.5 mM HEPES-KOH, pH 7.4, 35 mM glucose). Three sub-regions of the brain were dissected, and RNA was isolated using the NucleoSpin RNA XS kit (Macherey-Nagel, Germany) following the manufacture's protocol. The RNA quality and concentration were measured in the QIAxcel Advanced system (Qiagen, Germany) using QIAxcel RNA QC Kit v2.0 (Qiagen) and Qubit 3.0 fluorometer (Thermo Fisher Scientific, USA). The RNA samples with an RNA integrity score (RIS) value of more than eight were used in further processing. Ribosomal RNA was depleted from the total RNA using the Ribo-Zero Gold rRNA removal kit (Human/Mouse/Rat) (Illumina, USA). The ribo-depleted RNA was used to create a strand-specific RNA sequencing (ssRNA-seq) library, according to the TruSeq® Stranded Total RNA sample preparation guide.
GEO Accession
GSM4649193