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Each sample was combined with 500 µl of 2x buffer B (143 mM Tris pH 8.0, 143 mM NaCl, 14 mM EDTA and 5.7% SDS), 500 µl phenol chloroform, and approximately 0.25 g zirconium beads (0.1 mm, Biospec Products Inc).
Briefly, 1 µg of RNA from each sample was combined with 10X DNase reaction buffer and 1 U DNase I, mixed and incubated at RT for 15 min, followed by inactivation of DNase I by adding 1 µl of 25 µM EDTA.
Each sample was combined with the KnownSet into an ntegrated source data.
Phage samples were serially diluted into sterile water, and 100 μL of each sample was combined with 250 μL of fresh log phase bacterial culture with an optical density of 1.5 measured at 600 nm.
Briefly, 250 ng of total RNA from each sample was combined with Superscript II Reverse Transcriptase, TaqMan gene expression assays (Socs1, Mm00782550_s1; Txnrd1, Mm00443675_m1) and TaqMan Universal PCR Master mix.
Next, each sample was combined with 1/2 volume of Total exosome isolation (from cell media) reagent and mixed well by vortexing or pipetting up and down until a homogenous solution was formed.
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PCR products for each sample were combined and purified using a PCR cleanup kit (Invitrogen corp., Carlsbad, CA).
All three extracts for each sample were combined and lyophilized.
Equivalent amounts of RNA from each sample were combined per cultivar.
The vectors of the sorted CT values for each sample are combined into a matrix.
The labeled reaction products for each sample were combined and evaporated to dryness.
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