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Nanodrop 1000 detector

Manufactured by Thermo Fisher Scientific
Sourced in United States

The NanoDrop®-1000-Detector is a UV-Vis spectrophotometer designed for the quantification and purity analysis of nucleic acids and proteins. It utilizes a patented sample retention system that requires only 1-2 μL of sample to measure absorbance at multiple wavelengths.

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6 protocols using nanodrop 1000 detector

1

Modeling Acquired Resistance to EGFR-Targeted Therapies

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In vitro acquired resistance to gefitinib and afatinib was modeled by applying dose-escalation (up to 1 µM) of these compounds to PC9 cells. Afatinib resistant cells were exposed to a continuous (PC9-AR1) or a pulse (PC9-AR2) exposure. Genomic DNA was extracted using the Ambion®-RecoverAll kit (Life Technologies, Breda, The Netherlands). The quantity and purity of the extracted DNA were assessed at 260–280 nm with the NanoDrop®-1000-Detector (NanoDrop-Technologies, Wilmington, NC, USA), and EGFR, KRAS, BRAF, and PIK3CA mutational statuses were determined as previously described [17 (link)]. Nomenclature of EGFR mutations is reported in the Appendix A.
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2

Genotyping ANGPTL4 rs116843064 Polymorphism

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Genomic DNA was extracted from peripheral blood using a QIAamp-DNAMini-Kit (Qiagen, SanDiego, CA) and the manufacturer’s protocol. Using the NanoDrop®-1000-Detector (NanoDrop-Technologies, Wilmington, USA) the purity and concentration of DNAs were evaluated. The genotyping of the ANGPTL4 rs116843064 polymorphism was performed using Taqman®-probes-based assay. The PCR reaction was performed in a total volume of 12.5 μl through 10 ng DNA in TaqMan® Universal Master Mix with particular primes and probes (Applied Biosystems Foster City, CA). ABIPRISM tools with SDS-version 2.0 software has been used to examine the content of allelic samples.
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3

Genotyping rs1130233 Polymorphism via PCR

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Blood was collected into an Ethylene diamine tetra acetic acid (EDTA) anticoagulant tube from all subjects. Leukocyte DNA was extracted from the blood using a commercial kit (QIAamp® DNA Mini-Kit, Qiagen, San Diego, CA). The quantity and quality of DNA was evaluated using a Nano Drop®-1000-Detector (Nano Drop-Technologies, Wilmington,USA).17 (link) Genetic analysis for the rs1130233 polymorphism was performed using Taqman®-probes-based PCR reactions. This analysis was done using 20 ng of DNA, which was added to 6uL TaqMan® Universal Master Mix and 0.15uL specific primers were added. For evaluating the genotypes, the ABI-StepOne instruments (Applied Biosystems) with SDS version-2.0 software was used.
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4

Laser-Assisted Tissue Dissection and RNA Extraction

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Frozen tissue sections (5 μm) were thawed, fixed in 75% ethanol, and dehydratated in 100% ethanol and xylene. Neoplastic cells were then dissected using the laser microdissector Leica AS/LMD (Leica, Wetzlar, Germany). Laser-captured cells were pooled in lysis buffer and RNA was extracted with the QIAamp RNA Mini kit (Qiagen, San Diego, CA, USA). RNA was dissolved in DNase/RNase-free water, and measured by absorbance reading at 260/280 nm. RNA yields and integrity were checked at 260–280nm with NanoDrop®-1000-Detector (NanoDrop-Technologies, USA).
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5

Genotyping of Inflammation-Related SNPs

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Genomic DNA was extracted from blood samples at the Laboratory Medical Oncology (VUmc, Amsterdam, The Netherlands) using the QIAamp DNA Mini-Kit according to the manufacturer protocol (Qiagen, San Diego, CA). The concentration and purity of DNAs was determined with the NanoDrop-1000-Detector (NanoDrop-Technologies, Wilmington, USA). Genotype analysis of rs1800796, rs6136, and rs1130233 polymorphisms was performed using Taqman-based PCR reactions carried out in 12.5 µl total volume, using 20 ng of DNA diluted in TaqMan Universal Master Mix with specific primers and probes (SNP Genotyping Assays products C__11326893_10, C__11975277_20, and C__7489835_10, respectively). The ABIPRISM-7500 instrument (Applied Biosystems, Life Technologies, Foster City, CA) equipped with the SDS version-2.0 software was employed to evaluate the allelic content of each sample in the plate by reading the generated fluorescence.
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6

Genotyping ANGPTL3 Gene Variant

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DNA was extracted from a blood sample using the salting‐out extraction approach (Mardan‐Nik et al., 2019 (link)). The extracted DNA was assessed by the use of a NanoDrop®‐1000‐Detector (NanoDrop‐Technologies, Wilmington, DE, USA). Genotyping was undertaken for rs10789117 in the ANGPTL3 gene using the ARMS PCR (amplification refractory mutation system PCR). Tetra‐ARMS PCRs were undertaken in a 20 μL volume containing 2 μL of DNA samples, 10 μL of PCR Master Mix, 4.5 μL ddH2O, 0.5 μL for outer primers and 1.0 μL, 1.5 with the following primers (Forward outer primer 5′‐AAAACTCTCATAGGACATGTTTCAT‐3′; Forward inner primer 5′‐CCCTTTTATCTCTCT ACTACTTAATAACAA‐3′; Reverse outer primer 5′‐GAGGGTC AGTGTAGAAAAGATGA‐3′; Reverse inner primer 5′‐CCCTTTTATCTCTCTAC TACTTAATAACAA‐3′; Three band patterns were identified: 194 bp for AA, 291 bp for CC and 432 bp) (Table S1). Genotyping reagents were bought from Applied Biosystems (ABI‐Veriti 96‐well Thermal Cycler). The primers were designed using Primer‐1 and Oligo 7 version 7.24 software. PCR cycling protocols were 94°C for 5 min, 31 cycles at 94°C for 1 min, 56°C for 1 min, 72°C for 1 min, and a final extension at 72°C for 5 min. Gel electrophoresis was attempted using a 2% agarose gel. Finally, the genotypes were confirmed by Sanger sequencing as shown in Figure 1. All sequenced samples were analyzed using Finch TV version 1.4.0.
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