Supplementary material
TD
Supplementary Figure 1: A schematic representation of the RNA-Seq workflow. (A) The flowchart of RNA-Seq analysis outlines the experimental and data analysis steps carried out in the study. (B) The number of samples at collection timepoints and after quality-based filtering in each study arm.Supplementary Figure 2: Quality assessment of the RNA-seq data. (A-K) Plots to identify selection thresholds for quality-based filtering of samples. The distributions of (A-C) mapping of reads, (D) the number of reads uniquely mapped to the host, (E) the median coefficient of variation (CV) of gene coverage, (F-H) RNA integrity number (RIN) scores and (I-K) relative log expression plot of normalized counts help to identify samples that are outliers with metrics lying in the extreme value ranges. The final selection thresholds were as follows: number of reads uniquely mapped to the host >5M, median coefficient of variation (CV) coverage Supplementary Figure 3: Retrospective power analysis for each study arm. (A,C,E) Line plots for power vs. average normalized gene counts for DMPA-IM, LNG Implant and Cu-IUD. The stratified power is represented by each line for a certain sample size, stratified by the average counts of genes. Sample sizes varying from 5-50 are represented in different colors as shown in the legend in panel A. For a sample size greater than 40, the power is between 0.6 and 0.8 for genes with low counts (between 0 and 10) but improves significantly for genes with counts higher than 10 reads. (B,D,F) Marginal power-related results have been shown for each pair of sample sizes (SS1 and SS2), including marginal power, true discovery (TD), false discovery (FD), and false discovery cost (FDC, defined as the number of FD divided by the number of TD).Supplementary Figure 4: Principal component analysis (PCA) on paired-data from each study arm. PCA plots shown for each study arm, (A) DMPA-IM, (B) LNG Implant and (C) Cu-IUD. In each of the three plots, circles represent baseline samples and solid triangles represent month 1 samples.Supplementary Figure 5: Pathways enriched in at least one of the three study arms (DMPA-IM, LNG Implant and Cu-IUD) after 1 month of randomized contraceptive in post-vs-pre comparisons (nominal p-value <0.1). Dot plots to represent the statistical significance (nominal p-values) and normalized enrichment scores (NES) in gene set enrichment analysis (GSEA), for several MSigDB pathway collections have been shown. The statistical significance of the enriched pathways is shown by the size of the dots (1-ln (nominal p-value)), the larger the dot, the higher is the statistical significance. The normalized enrichment score (NES) is represented by a blue-to-red color-gradient, blue for negative scores and red for positive scores. The pathways are ordered by the nominal p-value of DMPA-IM vs. baseline contrast, with the most statistically significant pathway shown at the top.Supplementary Figure 6: Analysis on DMPA-IM subsets of participants with 