Mus musculus embryonic germ cell transcriptome

We crossed C57BL/6J-KitW-v (The Jackson Laboratory) males to WB/ReJ-KitW (The Jackson Laboratory) females to generate KitW/KitW-v compound heterozygotes, which are germ cell deficient, and control Kit+/Kit+ wild types. Two biological replicate ovaries and testes from KitW/KitW-v and Kit+/Kit+ embryos were collected at embryonic day 12.5, 14.5, and 16.5. Total RNA, of about 1 ug, was extracted using Trizol (Invitrogen) according to manufacturer’s instructions. Hemoglobin transcripts were selectively removed from total RNA by following GLOBINclear (Ambion) protocol recommendations. As per the Illumina kit protocol, poly-A-selected mRNA was used to generate mRNA-seq cDNA libraries using random hexamer-primers. cDNA fragments of ~200 nucleotides were isolated and modified for sequencing following the mRNA-seq protocol (Illumina). Illumina Genome Analyzer II was used to sequence 36-mers from the mRNA-seq libraries by following the manufacturer''s recommendations.