RNA Sequencing Analysis of villus tissues from unexplained recurrent spontaneous abortion patients and controls with induced abortions

Recurrent spontaneous abortion (RSA), defined as the failure of two or more consecutive clinical pregnancies before 20 weeks of gestation, affects approximately 1% of couples attempting to conceive. However, the underlying mechanisms of 50% of cases are unknown. The villus plays a crucial role during pregnancy, which can provide a delicate balance between immune tolerance and defense to maintain the pregnancy.We performed RNA-seq to identify gene expression alterations in the villus of RSA patients and controls. RNA-seq was done using TruSeq Stranded mRNA Library Preparation. Briefly, intact RNA was fragmented, end repaired, adapter ligation and PCR amplified following illumina protocol. Libraries were sequencing by illumins Hiseq 2000. After quality control, sequence data were processed with STAR to generate read alignments with hg19. Raw read counts for annotated genes were obtained with featureCounts with default settings, normalized and analyzed using DEseq2. Intact RNA isolated from 6 human decidua tissues was fragmented, end repaired, adapter ligation and PCR amplified following illumina protocol. Libraries were sequencing by illumins Hiseq 2000.