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The plugs were washed three times with 1 ml of TE, and pre-incubated in 300 µl (100 µl per plug) of TUNEL mix (1X TdT reaction buffer, 5 mM of CoCl2) for 30 min at room temperature.
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The agarose plugs were pre-equilibrated in 10 mM Tris-HCl, pH 8.0, 0.1 mM EDTA (5 ml per plug) for 30 min, followed by equilibration in 5 ml of 50 mM Tris-HCl pH 6.8, 5 mM MgCl2, and 10 mM β-mercaptoethanol for 30 min at room temperature.
By averaging mass spectra of 10 randomly selected plugs of verapamil water solution from the same experiment, we calculated the average intensity value per plug to be 435 ± 45 counts, indicating a 10% plug-to-plug variation.
The TUNEL mix was then removed and replaced with a fresh mix containing 2,400 U of TdT (800 U per plug) and 6 nmol of biotin-16-dUTP (2 nmol per plug) and the eppendorf tubes were incubated overnight at 4°C on a rotating wheel.
Three plugs were transferred into 2 ml eppendorf tubes and pre-incubated in 300 µl of NEB3 (ratio of 100 µl per plug, New England Biolabs) supplemented with 10 µg/ml of Rnase A for 30 min at 37°C in a water bath.
The third measure that we took to enhance the quality of the BIBAC library was the preparation of the DNA plugs at a proper concentration of DNA per plug.
Capillary formation was assessed by determining the percentage of CD31-positive Vybrant-labelled MPECs compared with the total number of CD31-positive cells within four randomly selected fields of view per plug.
The reaction buffer was withdrawn, replaced by fresh buffer containing 30 U of PciI per plug and the tubes were incubated for 4 h at 37°C in a water bath.
The DNA in the gel plugs was digested with 10 U of HindIII per plug at 37°C for 30 minutes.
The yeast cell pellets were treated with 1 mg/ml lyticase (70 U/mg) (Sigma, USA) for 2 hours and embedded in 1% low melting point agarose (MO BIO, USA) at a concentration of 2x10 cells per plug mold.
The cell mixture was transferred to plug molds (Biorad) with ∼80 ul of the cell suspension per plug (approximately 1.6×106 cells/plug).
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