Nanodrop lite spectrophotomer

Manufactured by Thermo Fisher Scientific

The NanoDrop Lite Spectrophotometer is a compact, easy-to-use instrument designed for the measurement of nucleic acid and protein concentrations. It utilizes a small sample volume to determine the absorbance of the sample, which is then used to calculate the concentration.

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Lab products found in correlation

Ethylene diamine tetraacetic acid (edta), by Merck Group (1 mentions) Micropulser apparatus, by Bio-Rad (1 mentions) Nucleospin plasmid kit, by Macherey-Nagel (1 mentions)

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NanoDrop (8392 citations) NanoDrop Lite (394 citations) NanoDrop spectrophotomer (2 citations)

5 protocols using nanodrop lite spectrophotomer

Quantifying Viral DNA Levels

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For HSV-2, 100 μL of viral
sample was combined with 100 μL of antiviral sample in a sterile
Eppendorf tube. A positive control was also included where 100 μL
of virus stock is mixed with 100 μL of sterile deionized water.
All samples were then incubated for 5 min at 37 °C in 5% CO₂. Following co-incubation of virus and antiviral, DNA concentrations
of each sample were measured using a NanoDrop Lite Spectrophotomer
(ThermoFisher Scientific). The DNA or RNA concentration of each sample
was noted. For DNA-genome viruses, 20 μL of 10× TURBO Dnase
Buffer was added to each sample. In the sample with the highest amount
of DNA (as measured by the spectrophotometer), 1 μL of TURBO
Dnase was added per 1 μg of DNA present. An equal volume of
TURBO Dnase was also added to all other samples in the batch. Samples
were then incubated for 30 min at 37 °C in 5% CO₂.
Finally, EDTA (Merck Life Sciences) was added to each sample at a
final concentration of 15 mM, and the samples were heated at 75 °C
for 10 min to deactivate the TURBO Dnase.

Jones L.M., Super E.H., Batt L.J., Gasbarri M., Coppola F., Bhebhe L.M., Cheesman B.T., Howe A.M., Král P., Coulston R, & Jones S.T. (2022). Broad-Spectrum Extracellular Antiviral Properties of Cucurbit[n]urils. ACS Infectious Diseases, 8(10), 2084-2095.

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Epididymal RNA Isolation Protocol

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The experimental animal at 4 months of age was euthanized by CO₂stunning, and an incision on lower abdomen was made to take out the male
reproductive tract. In the cold PBS buffer, the epididymis was separated from
the rest and was additionally divided into individual epididymal parts. The
caput epididymis was transferred to and washed in new cold PBS buffer and was
rapidly placed in liquid nitrogen. Frozen tissue was stored in –80℃ and was used
for total RNA isolation.
The extraction of total RNA was began with the homogenization of tissue in the
RNA extraction solution (iNtRON Biotech, Sungnam, Korea). The precipitation of
total RNA was carried out with the addition of isopropanol. After the washing in
70% DEPC-EtOH, total RNA pellet was air-dried and then resuspended in DEPC-
dH₂O. The amount and purity of total RNA isolated were calculated
with NanoDrop Lite spectrophotomer (Thermo Scientific, Wilmington, DE), and the
qualitative condition of total RNA was checked by 1.2% agarose gel
electrophoresis.

, & Lee K.H. (2017). Aberrant Expression of Cx Isoforms in the Adult Caput Epididymis exposed to Estradiol Benzoate or Flutamide at the Weaning. Development & Reproduction, 21(4), 379-389.

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Caput Epididymis RNA Extraction

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Once the animal became 4 months of postnatal age, anesthetization by
CO₂ stunning was performed. The male reproductive tract was taken
out from an incision on lower abdomen and was placed on the cold PBS solution.
The epi–didymis was first separated from the testis and other reproductive tract
and was further dissected into different epidi–dymal segments, including caput
epididymis. The tissue was briefly washed in fresh cold PBS solution once and
was quickly frozen in liquid nitrogen. The tissue was kept in –80℃ until
utilized for total RNA isolation.
To extract total RNA from the caput epididymis, the frozen tissue was completely
homogenized in total RNA extraction solution (iNtRON Biotech, Sungnam, Korea).
Total RNA was precipitated by isopropanol, and total RNA pellet was washed with
70% DEPC-EtOH. Then, air-dried total RNA was dissolved in DEPC- dH₂O.
The concentration of total RNA was assessed with NanoDrop Lite spectrophotomer
(Thermo Scientific, Wilmington, DE). The quality of total RNA was evaluated by
conventional agarose gel electrophoresis.

, & Lee K.H. (2017). Expressional Changes of Connexin Isoform Genes in the Rat Caput Epididymis Exposed to Flutamide or Estradiol Benzoate at the Early Postnatal Age. Development & Reproduction, 21(3), 317-325.

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Isolation and Characterization of Epididymal RNA

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The tissue was isolated from the experimental animals at 4 months of postnatal age. First, the
animals were euthanized by CO₂ stunning, and then an incision on lower abdomen was made
with a pair of scissors. The male reproductive tract was taken from the animal and was placed in the
cold PBS solution. The testis and epididymal fat were separated from the epididymis, and the
epididymis was quickly dissected into four different regions, such as initial segment, caput
epididymis, corpus epididymis, and caudal epididymis. Each part of the epididymis was rinsed in
fresh cold PBS solution and rapidly frozen in liquid nitrogen. The tissue was stored in
-80^oC until used for the isolation of total RNA.
The extraction of total RNA from collected caudal epididymis was carried out as following. The tissue
was homogenized in total RNA extraction solution (iNtRON Biotech, Sungnam, Korea) with a homogenizer
(Fisher Scientific, Pittsburgh, PA). Total RNA precipitated by isopropanol was washed with 70%
DEPC-treated EtOH , and air-dried total RNA pellet was resuspended in DEPC-treated RNase-free
dH₂O. The concentration and ratio of total RNA were measured with NanoDrop Lite
spectrophotomer (Thermo Scientific, Wilmington, DE). One microgram of total RNA was used to
determine the quality of the total RNA sample by agarose gel electrophoresis.

, & Lee K.H. (2016). Effects of Exposure to Estradiol Benzoate or Flutamide at the Weaning Age on Expression of Connexins in the Caudal Epididymis of Adult Rat. Development & Reproduction, 20(4), 349-357.

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Nucleic Acid Manipulation Protocols

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Standard nucleic acid manipulation techniques were carried out as described previously [45 ]. S. agalactiae genomic DNA and RNA purifications were performed as previously described [40 (link)]. Plasmids were purified from E. coli with a NucleoSpin Plasmid kit (Macherey‐Nagel), according to the manufacturer’s instructions. Nucleic acid concentrations were measured with a NanoDrop Lite Spectrophotomer (Thermo Scientific). The ratio of absorbance at 260 and 280 nm was used to check the purity of nucleic acids. Bacteria were transformed by electroporation with the Micropulser apparatus (Bio-Rad) and the Ec2 conditions (2.5 kV), as described by Dower for E. coli and by Ricci for S. agalactiae [46, 47 (link)].

Khazaal S., Al Safadi R., Osman D., Hiron A, & Gilot P. (2021). Investigation of the polyamine biosynthetic and transport capability of Streptococcus agalactiae: the non-essential PotABCD transporter. Microbiology, 167(12), 001124.

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