Supplementary files for De novo assembly and annotation of the vaginal metatranscriptome associated with bacterial vaginosis

Supplementary files for De novo assembly and annotation of the vaginal metatranscriptome associated with bacterial vaginosis

Supplementary Tables

Table S1. Summary of 40 samples used for transcriptome analyses associated with BV.

Table S2. 269 ribosomal sequences identified from vaginal transcriptome.

Table S3. 4,335 transfer RNA sequences identified from vaginal transcriptome.

Table S4. Classification of identified tRNAs.     

Table S5. Statistical summary of ORFs identified by different programs.

Assembly indicates total number of reads obtained from 40 different transcriptomes.

Each accession number indicates the number of reads from the given transcriptome.

Table S6. Identified taxonomy with accumulated contig size from vaginal transcriptome.

Table S7. Number of mapped reads on identified bacterial taxonomy in each sample.

Table S8. Statistical summary of mapping results on identified vaginal contigs in each sample.

Table S9. Differentially expressed COGs in BV-associated group as compared to non-BV-associated group.

Differentially expressed COGs were identified based on adjusted P-values less than 0.01 and two fold changes.

Numbers indicate the normalized expression value of identified COGs in each sample by DESeq2.

Table S10. Number of identified COGs assigned to 27 functional categories in up- and down-regulated groups.

Table S11. Differentially expressed KEGG enzymes in BV-associated group as compared to non-BV-associated group.

Table S12. Number of identified enzymes assigned to 315 KEGG pathways in up- and down-regulated groups.

Table S13. Summary of 176 assembled bins from 40 vaginal transcriptome datasets.

Table S14. Normalized abundance of identified bacteria according to taxonomy for individual bin in each sample.

Table S15. Identified bacterial species in three different approaches: 16S rRNA amplicon, metaT-Kraken, and metaT-Assembly.

Supplementary Figures

Figure S1. Number of vaginal samples collected from each of 14 patients.

Figure S2. Relative abundance of identified bacteria in 40 different samples at phylum level.

Figure S3. Relative abundance of 176 bins in 40 different samples at genus level. Yellow and purple bars indicate positive and negative samples for BV state, respectively.

Figure S4. Relative abundance of 176 bins in 40 different samples at species level. Yellow and purple bars indicate positive and negative samples for BV state, respectively.

Figure S5. Comparison of number of identified bacterial species from three different studies.

16S rRNA indicates the previous study using 16S rRNA amplicon sequencing from 96 samples. metaT-Kraken indicates the previous study using metatranscriptomic data from 40 samples using Kraken. metaT-Assembly indicates this study using metatranscriptomic data from 40 samples using de novo transcriptome assembly followed by BLASTX search against an NR protein database.