Transcriptome profiles of Lhx2 knockout developing mouse gonads

Male and female Lhx2lox/lox mice with a tamoxifen inductible Cre were crossed . As control group were Lhx2lox/lox mice without the tamoxifen inductible Cre.The pregnant females in both the groups were fed with tamoxifen on E9.5 The embryos were collected on E11.5 and E12.5. The gonads were separated from the mesonephros and preserved in RNA later. The sex of the mebryos weas determined by PCR. RNA was extracted from 30 pairs of gonads of each sex and each genotype and RNA sequencing was performed using Illumina NextSeq 500 platform. Illumina TruSeq adapters were used; the read length was 76 nucleotides and was paired at both ends. An average of 45 million raw reads was generated per sample. Alignment was done using Tophat-2.0.13 using mm84 sequence as reference (ftp://ftp.ensembl.org/pub/release-84/fasta/mus_musculus/dna/).