GSM5507776: IBPL1_E; Mus musculus; RNA-Seq
For gene expression analyses of the choroid plexus, the lateral choroid plexuses (LCPs) from adult mice were dissected out and snap frozen. The animals were euthanized by CO2 and cervical dislocation around 10 am when the females were in proestrus. mRNA isolation was performed using the Quick-RNA Microprep Kit (Zymo Research, R1050) according to the manufacturer's instructions. The mRNA samples were processed for sequencing at QB3 Vincent J. Coates Genomics Sequencing Laboratory, UC Berkeley. The LCP mRNA was enriched for using Oligo dT beads from the Invitrogen Dynabeads mRNA Direct kit (61011). Subsequent library preparation steps of fragmentation, adapter ligation, and cDNA synthesis were done on the enriched mRNA using the KAPA RNA HyperPrep kit (Roche, KK8540). Truncated universal stub adapters were used for ligation, and indexed primers were used during PCR amplification to complete the adapters and to enrich the libraries for adapter-ligated fragments. Samples were checked for quality on an AATI (now Agilent) Fragment Analyzer. Libraries were then quantified using qPCR on a BioRad CFX Connect to measure molarity of only sequence-able molecules using the Kapa Biosystems Universal Illumina quant kit, pooled equimolar, clustered at 3nM with 2% PhiX v3 control library spike-in, and sequenced as a 100bp paired end run on an Illumina HiSeq 4000. Bcl files were then converted to fastq format and demultiplexed using the innate bcl2fastq v1.19 software.