Additional file 10: of Isolated C. elegans germ nuclei exhibit distinct genomic profiles of histone modification and gene expression

IGN and soma RNA-seq expression analysis (XLSX 4868 kb

Additional file 8: of Isolated C. elegans germ nuclei exhibit distinct genomic profiles of histone modification and gene expression

Figure S8 Heatmap of H3K4me3 levels for genes with tissue-enriched expression. Heatmap displaying the levels of H3K4me3 for genes with SOM-enriched expression or IGN-enriched expression, as assayed by IGN H3K4me3 ChIP-seq and SOM H3K4me3 ChIP-seq. (PDF 3310 kb

Additional file 9: of Isolated C. elegans germ nuclei exhibit distinct genomic profiles of histone modification and gene expression

Table S1 Quantification of fraction of germline nuclei (DOCX 14 kb

Additional file 14: of Isolated C. elegans germ nuclei exhibit distinct genomic profiles of histone modification and gene expression

IGN_H3K4me3_q0.001_peaks_ce10 (XLSX 3928 kb

Additional file 13: of Isolated C. elegans germ nuclei exhibit distinct genomic profiles of histone modification and gene expression

SOM_H3K27ac_q0.001_peaks_ce10 (XLSX 5600 kb

Additional file 7: of Isolated C. elegans germ nuclei exhibit distinct genomic profiles of histone modification and gene expression

Figure S7 Confirmation of germline-enriched H3K27ac modification in isolated germ nuclei by ChIP-qPCR. Two previously characterized germline-expressed (him-3 and oef-1) and soma-expressed genes (elt-2 and myo-3) were examined for abundance of H3K27ac in IGN by ChIP-qPCR. Three sets of primers were tested for each germline-specific gene. C37H5.15 served as positive control. Elt-2 served as negative control and was used to calculate fold enrichment. ChIP results are expressed as percent of input using Ct values (A) and fold enrichment of H3K27ac modification normalized to elt-2 (B). (PDF 1136 kb

Additional file 16: of Isolated C. elegans germ nuclei exhibit distinct genomic profiles of histone modification and gene expression

SOM-CHIP for IGN-enriched expression (XLSX 838 kb

Additional file 3: of Isolated C. elegans germ nuclei exhibit distinct genomic profiles of histone modification and gene expression

Figure S3 DEseq2 analysis of gene expression levels in SOM and IGN. (A) MA plot showing the differential gene expression pattern for SOM and IGN samples. The differentially expressed genes between SOM and IGN were represented with red dots (p adj < 0.01). Y-axis: M (log2TPM (fold change)). X-axis: A (Mean of normalized counts). (B) PCA analysis indicating good correlation between replicates for SOM and IGN samples. (C) Venn diagrams displaying the overlap between Cuffdiff-called and DESeq2-called differentially expressed genes in SOM (top) and IGN (bottom) samples. Of the Cuffdiff-called differentially expressed genes in SOM or IGN, 91.48% or 86.42% were also called by DESeq2, respectively. (D) Boxplot exhibiting the significance of differentially expressed gene sets either called by both Cuffdiff and DESeq2 or DESeq2 only. (E) Boxplot displaying the overall gene expression (TPM) for tissue-enriched transcripts identified by Cuffdiff. Transcripts with less than 10 total read counts across all the samples were removed for TPM analysis. Thus, 3941 out of 3965 SOM-enriched transcripts (blue) or 4940 out of 5075 IGN-enriched transcripts (red) in either SOM RNA-seq or IGN RNA-seq were analyzed. Each box indicates the median and interquartile range of TPM level. (PDF 941 kb

Additional file 1: of Isolated C. elegans germ nuclei exhibit distinct genomic profiles of histone modification and gene expression

Figure S1 Isolated germline nuclei from a second germline transgenic strain. (A) Young adult pie-1p::GFP::H2B transgenic worm showing germline expression. GFP::H2B is expressed in the nuclei of germ cells at all developmental stages, including oocytes and embryos. (B) Isolated nuclei from pie-1p::GFP::H2B young adult worms were immunostained with GFP (green) and stained with DAPI (blue). Nuclei stained with both GFP and DAPI (89.1%, n = 2111) were considered germline nuclei. Two independent experiments were performed. (C) Isolated nuclei from wild type VC2010 N2 young adult worms were immunostained with GFP (green) and stained with DAPI (Blue). Scale bars, 20 μm in (A), 5 μm in (B) and (C). (PDF 6536 kb

Additional file 12: of Isolated C. elegans germ nuclei exhibit distinct genomic profiles of histone modification and gene expression

IGN_H3K27ac_q0.001_peaks_ce10 (XLSX 5606 kb