Transcriptomic analysis of femoral diaphysis and primary osteoprogenitor cells cultures from mouse strains with SHIP1 deficiency and controls
Transcriptomic analysis of femoral diaphysis and primary osteoprogenitor cells cultures from mouse strains with SHIP1 deficiency and controls
RNA was isolated from the diaphysis of one femur per mouse that was homogenized in TRIzol® (n=3 for each of the following mouse genotypes: SHIPstyx/styx, SHIP1+/styx, wild-type (C57BL6/J), Rag2-/-/Il2rg-/-/SHIP1styx/styx, Rag2-/-/Il2rg-/-/SHIP1+styx, and Rag2-/-/Il2rg-/-/SHIP1+/+). Alternatively, total RNA was extracted using the NucleoSpin® RNA Plus Kit from primary osteoclast cultures supplemented or not with RANKL (n=3 for each genotype indicated above). RNA was isolated according to the manufacturer's instructions and RNA concentration and integrity were assessed using a Thermo Fisher Scientific Qubit 4.0 fluorometer with the Qubit RNA BR Assay Kit (Thermo Fisher Scientific, Q10211) and an Advanced Analytical Fragment Analyzer System using a Fragment Analyzer RNA Kit (Agilent, DNF-471), respectively.  Sequencing libraries were made with 1000 ng input RNA using an illumina TruSeq Stranded mRNA Library Prep kit (illumina, 20020595) in combination with TruSeq RNA UD Indexes (illumina, 20022371) according to illumina's guidelines.