listeria_metagenomic

For files are provided :

• The count matrix corresponds to the number of amplicons mapped per OTU for each sample
• The annotation matrix corresponds to the taxonomical annotation of each OTU
• The target matrix provides the experimental design
• The contrast file correspond to the deseq2 model These data can be re-analysed and visualize with shaman.cb3i.pasteur.fr. Warning : It is nessary to indicate as interaction in this exact order :

1. condition:mice
2. condition:time

Of note:

• Reads data are provided here : http://www.ebi.ac.uk/ena/data/view/PRJEB13646
• "m" samples correspond to T0 samples that were obtained by adding 2 Day and 1 Day before infection counts as following WT.m2: WT2.2 WT2.20

WT.m3:
WT3.3 WT3.21

WT.m4
WT4.4 WT4.22

WT.m5
WT5.5

Delta.m7
Delta1.7 Delta1.25

Delta.m8
Delta2.8 Delta2.26

Delta.m9
Delta3.9 Delta3.27

Delta.m11
Delta5.11 Delta5.29

Delta.Compl.m13
Delta.Compl1.13 Delta.Compl1.31

Delta.Compl.m15
Delta.Compl3.15 Delta.Compl3.33

Delta.Compl.m16
Delta.Compl4.16 Delta.Compl4.34

Delta.Compl.m17
Delta.Compl5.17 Delta.Compl5.29