### README

# This is a key to the supplementary tables provided as part of "The transcriptomic response to a short day to long day shift in the reference legume Medicago truncatula" by Thomson et al. (2018).

Supplemental_Table_S_1_TPM.csv
	Observations: 907,992
	Variables: 5
		gene - Gene ID corresoponding to Mt4.0v2 genome annotation
		TPM - Gene abundance in Transcripts per Million
		condition - Growth condition (i.e. SD or LD)
		time - The timepoint of sampling (i.e. 0, 2 or 4)
		replicate - biological replicate (i.e. 1, 2 or 3)

Supplemental_Table_S_2_RT_qPCR_Primers.csv
	Observations: 12
	Variables: 2
		Primer   - Primer 
		Sequence - Primer sequence

Supplemental_Table_S_3_Individual_timepoint_analysis.csv
	Observations: 19,600
	Variables: 9
		timepoint - The timepoint of sampling (i.e. ZT+0, ZT+2, ZT+4)
		gene - Gene ID corresoponding to Mt4.0v2 genome annotation
		baseMean  - The mean number of normalized counts for this gene across all libraries
		log2FoldChange - The log2 fold-change in LD conditions relative to SD
		lfcSE - The log2 fold-change standard error
		stat - The Wald significance test statistic
		pvalue - The Wald significance test p-value
		padj - The re-calculated adjusted p-value (false discovery rate) for the 85642 Wald significance tests accross all three timepoints
		description - The Mt4.0v2 genome annotation gene description

Supplemental_Table_S_4_DE_pattern_genes.csv
	Observations: 31,363
	Variables: 3
		gene - Gene ID corresoponding to Mt4.0v2 genome annotation
		baseMean - the mean number of normalized counts for this gene across all libraries
		padj - The adjusted p-value (false discovery rate) for the interaction term from the likelihood ratio test

Supplemental_Table_S_5_DE_pattern_contrasts.csv
	Observations: 28,548
	Variables: 9
		timepoint - The timepoint of sampling (i.e. ZT+0, ZT+2, ZT+4)
		gene - Gene ID corresoponding to Mt4.0v2 genome annotation
		baseMean - The mean number of normalized counts for this gene across all libraries
		effectSize - The mean difference between LD and SD in TPM
		log2FoldChange - The log2 fold-change in LD conditions relative to SD
		lfcSE - The log2 fold-change standard error
		stat - The Wald significance test statistic
		padj - The re-calculated adjusted p-value (false discovery rate) for Wald significance test from the 9,516 DE genes across the three timepoints
		description - The Mt4.0v2 genome annotation gene description

Supplemental_Table_S_6_DE_pattern_clusters.csv
	Observations: 57,096
	Variables: 7
		gene - Gene ID corresoponding to Mt4.0v2 genome annotation
		cluster - The cluster (1-18) this gene is assigned to
		condition - Growth condition (i.e. SD or LD)
		time - The timepoint of sampling (i.e. 0, 2 or 4)
		std_TPM - Standardised gene abundances 
		membership - C-means clustering membership score
                description - The Mt4.0v2 genome annotation gene description

Supplemental_Table_S_7_DE_magnitude_genes.csv
	Observations: 31,363
	Variables: 3
		gene - Gene ID corresoponding to Mt4.0v2 genome annotation
		baseMean - The mean number of normalized counts for this gene across all libraries
		padj - The adjusted p-value (false discovery rate) for the interaction term from the Wald significance test

Supplemental_Table_S_8_DE_magnitude_contrasts.csv
	Observations: 14,082
	Variables: 10
		timepoint - The timepoint of sampling (i.e. ZT+0, ZT+2, ZT+4)
		gene - Gene ID corresoponding to Mt4.0v2 genome annotation
		baseMean - The mean number of normalized counts for this gene across all libraries
		effectSize - The mean difference between LD and SD in TPM
		log2FoldChange - The log2 fold-change in LD conditions relative to SD
		lfcSE - The log2 fold-change standard error
		stat - The Wald significance test statistic
		padj - The re-calculated adjusted p-value (false discovery rate) for Wald significance test from the 4,694 DE genes across the three timepoints
		description - The Mt4.0v2 genome annotation gene description
		group - Statistically different expression at a given timepoint (ZT0, ZT2 or ZT4) and the direction ot this expression in LD relative to SD (u = up; d = down). If time point is absent the gene is not differentially expressed at this timepoint. Note there is no fold-change or read depth filtering applied.

Supplemental_Table_S_9_DE_magnitude_clusters.csv
	Observations: 28,164
	Variables: 6
		gene - Gene ID corresoponding to Mt4.0v2 genome annotation
		cluster - The cluster (1-18) this gene is assigned to
		condition - Growth condition (i.e. SD or LD)
		time - The timepoint of sampling (i.e. 0, 2 or 4)
		std_TPM - Standardised gene abundances 
		membership - C-means clustering membership score
                description - The Mt4.0v2 genome annotation gene description