Pelagomonas calceolata gene expression levels in different nitrogen conditions and differential expression analysis.

These files contains the expression levels and DESeq2 results of Pelagomonas calceolata genes cultivated with different nitrate conditions. Two strains of P. calceolata (RCC100 and RCC697)  were cultivated and their RNAs reads were aligned on the predicted genes of P. calceolata RCC100 genome: https://www.ncbi.nlm.nih.gov/Traces/wgs/CAKKNE01?display=download

The following culture conditions were analysed :

882 µM of Nitrate (RCC100 and RCC697) 

441 µM of Nitrate (RCC100)

220 µM of Nitrate (RCC100 and RCC697)

50 µM of Nitrate (RCC697)

882 µM Cyanate (RCC100)

882 µM Ammonia (RCC100)

441 µM Urea (RCC100)

20230427_RCC100-Nitrate_transcriptomes_rawcounts.tsv : the file contains the raw read counts of RCC100 in 6 culture conditions in triplicate + the gene names = 19 columns.

20230427_RCC100-Nitrate_transcriptomes_TPM.tsv : same data normalized in transcript per kb per million mapped reads (TPM).

20230427_RCC697-Nitrate_transcriptomes_rawcounts.tsv : the file contains the raw read counts of RCC697 of 3 culture conditions in triplicate + the gene names = 10 columns.

20230427_RCC697-Nitrate_transcriptomes_TPM.tsv : same data normalized in transcript per kb per million mapped reads (TPM).

Differential expression analysis (DESeq2) was performed by pairwise comparisons between the standard condition (882 µM nitrate) and low-nitrate conditions (50, 220 or 441 µM nitrate) or changing nitrogen sources (882 µM ammonium, 882 µM cyanate and 441 µM urea). Each DESeq-results_RCCxxx_xxx.tsv file contains 6 columns : P.calceolata gene name, base Mean, log2 Fold Change, standard error value (lfcSE), pvalue and adjusted pvalue (padj).