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The antisense RNA probes were digoxin/digoxigenin labeled, diluted in hybridization buffer and hybridized on 10 μm tissue cryosections overnight in a humidified stove at 62°C.
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Additional confirmation of the conjugation efficiency of SBD to fluorescent labels was carried out by fluorescence correlation spectroscopic (FCS) measurement of diffusion times of the uncoupled fluorescent label diluted to ∼1 nM.
Complexes 1 and 2 showed similar retention in all cell lines with 10 20-fold 10 20-foldel diluted after 72 h.
The cellular retention of 3 was highly cell line dependent with 36-fold of the label diluted in HeLa cells, 105-fold in MDA-MB-231-mcherry cells, and 1000-fold iNIH/3T3T3 cells.
After a short rinse in PBS (3 times 5 min each), samples were incubated with a 10 nm gold-conjugated secondary antibodies (goat and rat IgG for ascorbate labeling and goat anti rabbit IgG for glutathione labeling) diluted 1 50 (for sections incubated with the glutathione antibody) and 1 100 (for sections incubated with the ascorbate antibody) in PBS for 90 min at RT.
Then, pre-hybridization solution was removed and replaced by one (for single FISH or CISH), two (for double FISH or FISH/CISH) or three cRNA probes of interest (for double FISH/CISH triple labeling) diluted in pre-hybridization solution at appropriate concentrations.
Subsequently 0.5 µg of biotin labeled DBS diluted in 50 µl 1X GMS buffer was added in the well and incubated at 4°C for 1 hour.
The PSIM protocol consists in spotting small-volume droplets (30 nl) of fluorescent labeled proteins, diluted in a wide range of concentrations, on the sample surfaces under investigation.
15 μl of anti-HA monoclonal antibody (Alexa Fluor labeled MonoHA) diluted 1 250 times was added and incubated for 2 h at room temperature.
Blots were then washed and incubated 1 h with secondary anti-human (or anti-mouse or anti-rabbit) HRP labeled antibodies (diluted at 1/10000 in PBS 0.1% Tween 20) (Jakson ImmunoResearch Laboratories, Westgrove, PA, USA).
The labeled and diluted target oligodeoxyribonucleotide samples with or without background cDNA were hybridized to our custom microarrays at 45°C for 16 h in a Hybridization Oven 640 (Affymetrix) set at 60 rpm under standard conditions.
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