Dual 3’Seq using deepSuperSAGE uncovers transcriptomes of interacting Salmonella enterica Typhimurium and human host cells

Table 2 Summary of the rRNA depletion of total RNA from separately cultivated cells and interaction stages

Cells and interaction stages	Input amount of total RNA	Applied Ribo-Zero rRNA Removal Kit(s)	No. of reactions
SL1344	5 μg	Gram-Negative Bacteria	1
HeLa-S3	15 μg	Human/Mouse/Rat	3
Early interaction*	50 μg	Human/Mouse/Rat	10
Early interaction*	50 μg	Gram-Negative Bacteria	2
Mid-level Interaction	20 μg	Human/Mouse/Rat	4
Mid-level Interaction	20 μg	Gram-Negative Bacteria	1
Late Interaction	20 μg	Human/Mouse/Rat	4
Late Interaction	20 μg	Gram-Negative Bacteria	1

*Two fifth of the depleted total RNA from early interacting cells were used for preparation of deepSuperSAGE and MACE libraries, respectively. The remaining fifth was kept for subsequent qRT-PCR validation.
Total RNA from cultivated HeLa-S3 and SL1344 cells was depleted with the correspondent Ribo-Zero rRNA Removal Kit, while RNA derived from infection assays was successively treated with both kit versions. The number of reactions for each type of kit reflects the depleted amount of rRNA in prokaryotic or eukaryotic samples. One reaction is sufficient to deplete 5 μg of the designated input total RNA.

ISSN: 1471-2164