title: RNA-seq of mus musculus: day 11.5 embryos : Sample M25_S9
design: Total RNA was harvest from embryos as described above. Ribosomal RNA was depleted using the RiboZero™ Magnetic Kit (Human/Mouse/Rat) from Illumina. Libraries were prepared from the Ribo-depleted RNA using the NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (New England BioLabs) with the following modifications: Ribo-depleted RNA was fragmented for 5 min at 94°C to obtain >300bp fragments and first strand synthesis reaction was incubated for 50 min at 42°C. PCR Library enrichment was performed using the KAPA HiFi DNA Polymerase (KAPA Biosystems) with Illumina barcoded sequencing primers. Library size distribution was confirmed on an Agilent 2100 Bioanalyzer with a High Sensitivity DNA Chip (Agilent Technologies). Barcoded libraries were combined and sequenced with an Illumina NextSeq, resulting in approximately 60 million paired-end 150-base pair sequencing reads per embryo.