Supplemental_Guide - This file which provides a guide to each of the supplementary files

Supplemental_Methods - Detailed laboratory and analysis methods to supplement descriptions in paper

Supplemental_Table_S1 Sample data sets.xlsx - List of all samples included in paper including numbers of reads, number of confirmed
       SLs, number of confirmed polyAs, number of wormbase genes at various thresholds, and SRA accessions

Supplemental_Table_S2 expression of wormbase_genes.readcounts_dcpm_per_sample.gz - Read counts and dcpm for all wormbase genes for all samples

Supplemental_Table_S3 Change point Embryonic_Gene_Expression_Segments.gz - Analysis of up- and down-regulated genes by change point analysis

Supplemental_Table_S4 Differential_Expression_Using_EdgeR.xlsx - Up- and down-regulated gene counts, by common name, top 20 up and down regulated 
       genes by name and category, up and down regulated genes by gene family

Supplemental_Table_S5 FullGO.xlsx - GO terms enriched in each up- and down-regulated gene set

Supplemental_Table_S6 GOcluster_Fig2D.xlsx - GO terms enriched in each cluster; full gene list of all genes up- and down-regulated by cluster

Supplemental_Table_S7 change points of TF cascades.docx - Change points of transcription factors in regulatory cascades

Supplemental_Table_S8a Alternatively_spliced_major_form_dominant.txt.gz - List of splice forma for which the major form predominates

Supplemental_Table_S8b Alternatively_spliced_minor_form_dominant.txt.gz - List of splice forma for which the minor form predominates

Supplemental_Table_S9 All_introns_maxexpression_maxorf_readcount_reads_per_million_per_sample.ws225.gz - All introns with their maximum
       expression in any sampl, maximum ORF length in any sample, as well as read count and reads per million for each sample

Supplemental_Table_S10 All_exons.readcounts_dcpm_per_sample.gz - All exons with their read count and dcpm (expression level, depth of coverage per million
       reads) per sample

Supplemental_Table_S11 Histone genes and patterns.xlsx - List of histone genes, their type, posotion, mate, cluster, motify, type and expression pattern

Supplemental_Table_S12 Unified_dcpm_per_ncRNA_pseudogene.gz - The dcpm (expression level, depth of coverage per million reads) for each WormBase annotated ncRNA
       and pseudogene per sample for the unified time series.

Supplemental_Table_S13 Unified_dcpm_per_wormbase_gene.gz - The dcpm (expression level, depth of coverage per million reads) for each WormBase annotated gene.

Supplemental_Table_S14 Above_threshold_blocks.xlsx - blocks of above threshold coverage that were not contiguous with WormBase exons for both the aggregate projects and only the polyA+ projects.

Supplemental_Fig_S1 - Nuclear counts per sample

Supplemental_Fig_S2 - Relationship between the samples of the four time series and the unified values for conversion of relative scale to embryonic time

Supplemental_Fig_S3 - Correlation of time series with single embryo data (Hashimshony et al., 2015)

Supplemental_Fig_S4 - Total genes with at least 0.02 dcpm at each stage

Supplemental_Fig_S5 - Genes increasing and decreasing in expression at each stage by change-point and edgeR analysis

Supplemental_Fig_S6 - Expression patterns of gene families, number of up- and down-regulated genes between adjacent stages

Supplemental_Fig_S7 - GO analysis: GO enrichment for all the genes found to be up- and down-regulated at each time point, 
	     each edgeR annotated comparison and each set of maximally expressed genes. We then calculated the Spearman correlation 
	     for the GO term enrichment for each time point and comparisons. 

Supplemental_Fig_S8 - Venn diagram of the overlap of detected splice junctions with WormBase junctions

Supplemental_Fig_S9 - Number of splice junctions confirmed in each sample at a dcpm threshold of 0.03 and 0.07 

Supplemental_Fig_S10 - Number of unique introns per sample

Supplemental_Fig_S11 - Representation of splice junctions overlapping and outside WormBase gene models

Supplemental_Fig_S12 - Ratio of minor to major splice isoforms

Supplemental_Fig_S13 - Operon bin dynamics. Operons were binned according to the ratio of SL2/(SL2+SL1) at the second gene (G2) in the operon.

Supplemental_Fig_S14 - Average ChIP-seq signal surrounding the transcript start site of the first (left) and second (right) gene in all operons.

Supplemental_Fig_S15 - DNA sequence motifs in the intergenic sequence between divergently transcribed histone genes

Supplemental_Fig_S16 - Average dcpm values for 80kb regions for bases annotated as intergenic, protein coding gene, or non-coding gene in each 80kb region.

Supplemental_Fig_S17 - Read coverage adjacent to the 5’ and 3’ edges of transcripts.