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Sds 2.3 software package

Manufactured by Thermo Fisher Scientific
Sourced in United States

The SDS 2.3 software package is a data analysis tool designed for use with Thermo Fisher Scientific's analytical instrumentation. The software's core function is to provide users with the ability to process, visualize, and manage data generated from various laboratory experiments and analyses.

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7 protocols using sds 2.3 software package

1

RNA Extraction and qPCR Analysis in Cynomolgus Monkeys

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For RNA extraction, 5 mL of blood was taken from the femoral vein of cynomolgus monkeys after fasting for 14‐16 hours. White blood cells were extracted from the blood,13 and total RNA was extracted using the TRIzol method.14, 15, 16 Then, cDNA was synthesized from 2 μg of total RNA using the EasyScript First‐Strand cDNA Bio‐Synthesis SuperMix (TransGen Biotech) and oligo‐dT primers (Invitrogen).
Each DNA sample was amplified by PCR amplification in a 20 μL volume containing 10 μL of SYBR® Premix Ex TaqTM (2 × ), 0.4 μL of the forward primer (10 μmmol/L), 0.4 μL of the reverse primer (10 μmmol/L), 2 μL of cDNA as the template DNA, and 7.2 μL of ddH2O. The amplification and analysis were performed using an ABI StepOne Real‐Time PCR System and the SDS 2.3 software package (Applied Biosystems). The PCR conditions were as follows: after the initial denaturation at 95°C for 5 minutes, we performed a denaturing step at 95°C for 5 seconds and an annealing step at 60°C for 34 seconds for 40 cycles. A dissociation stage followed the system default setting at 95°C for 15 seconds, 60°C for 1 minute and then 95°C for 15 seconds.
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2

Validating Microarray Data with qRT-PCR

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Microarray data were validated by quantitative reverse-transcription polymerase chain reaction (qRT-PCR) using 3 independent biological samples of freshly isolated Sca-1 cells. In addition to selected genes (Bdnf, Ccl19, Ccl9, Crlf1, Cxcl13, Ptn, Sfrp2, Spp1, Wisp2), ß-actin (Actb) was used as endogenous control. PCR amplification was performed using a 7900 HT Sequence Detection System (Applied Biosystems, CA, USA). Thermal cycling was as follows: 2 minutes at 50°C; 10 minutes at 95°C, followed by 15 seconds at 95°C; and 1 minute at 60°C for 45 cycles. Real-time PCR data were quantified using the SDS2.3 software package (Applied Biosystems) followed by relative quantification using the comparative Ct method (ΔΔCt method)[20 (link)] (S1 Table).
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3

Genotyping DNA Repair Gene Polymorphisms

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Based on information in the NCBI SNP database and the International HapMap project data for the Han Chinese population and previous studies on DNA repair genes [16 (link),17 (link),18 (link),19 (link)], the polymorphisms of rs25487 (XRCC1), rs4462560 (NEIL1) and rs12645561 (NEIL3) were selected. Fasting venous blood (10 mL, EDTA anticoagulant) was harvested from patients and controls. According to a standard protocol, total DNA from leukocytes was extracted using the salt fractionation method [20 (link)]. Single nucleotide polymorphism genotyping was performed with the TaqMan allelic discrimination assay on ABI PRISM 7900HT Sequence Detection system (Applied Biosystems, San Diego, CA, USA). Each genotyping assay contained one pair of primers and one pair of probes (sequences provided in Appendix ATable A1). Amplification was performed under the following conditions: 50 °C for 2 min, 95 °C for 10 min followed by 45 cycles of 95 °C for 15 s and 60 °C for 1 min. For quality control, five repeated samples and two blank controls were assigned into each 384-well format. The genotyping results were calculated by the allelic discrimination mode of the SDS 2.3 software package (Applied Biosystems, Foster City, CA, USA), and a 100% concordant was achieved.
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4

Genotyping of Genetic Variants

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Fasting venous blood was drawn from patients and controls. The total DNA of leukocytes was extracted by salt fractionation. The ABI PRISM 7900HT sequence detection system (Applied Biosystems, CA, USA) and the TaqMan allele identification method were used for SNP genotyping. Each 384-well format is allocated five replicate samples and two blank controls for quality control. The allelic discrimination model of the SDS 2.3 software package (Applied Biosystems) was used to calculate the genotyping results.
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5

Genotyping of Genetic Polymorphisms

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Genomic DNA was extracted from peripheral blood mononuclear cells using protease K digestion and phenol-chloroform purification. The polymorphisms of rs23544, rs3135029, rs1050391 and rs1063478 were genotyped by the TaqMan allelic discrimination assay on ABI PRISM 7900HT Sequence Detection system (Applied Biosystems, San Diego, CA, USA). The primers used for genotyping are listed in Supplementary Materials Table S1. The genotyping results were determined by the allelic discrimination mode of the SDS 2.3 software package (Applied Biosystems, Foster City, CA, USA), and a 100% concordant was achieved.
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6

Genetic Polymorphism Profiling in Chinese

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Based on information in the NCBI SNP database and the International HapMap project data for the Han Chinese population, the polymorphisms of NOX4 rs11018628, MTHFR rs1801133 and NEIL3 rs12645561 were selected. Blood samples were collected after a 12 h overnight fasting period and then separated into serum, red blood cells, and buffy coat. Total DNA from leukocytes was extracted using the salt fractionation method according to a standard protocol (15 (link)). DNA samples were subjected to DNA genotyping using the TaqMan SNP Genotyping Assay (Applied Biosystems; Thermo Fisher Scientific, Inc., Waltham, MA, USA). Briefly, each genotyping assay contained one pair of primers and one pair of probes (Table I). The PCR conditions were 50°C for 2 min, 95°C for 10 min followed by 45 cycles of 95°C for 15 sec and 60°C for 1 min. The genotyping results were calculated by the allelic discrimination mode of the SDS 2.3 software package (Applied Biosystems; Thermo Fisher Scientific, Inc.), and a 100% concordance was achieved.
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7

Quantification of Serum Viral Load and Genotyping

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Total DNA from leukocytes was extracted by the phenol-chloroform method according to a standard protocol. 19 Serum viral load of all treated patients was quantified at baseline, weeks 4, 12, 24, 48 and 24 after cessation of treatment by Cobas Amplicor HCV Monitor Test (v2.0, Roche, Basel, Switzerland). The polymorphisms of rs4273729 (G4C) and IL28B rs12980275 (A4G) were genotyped by the TaqMan allelic discrimination assay on ABI PRISM 7900HT Sequence Detection system (Applied Biosystems, San Diego, CA, USA). Each genotyping assay contained one pair of primers and one pair of probes (sequences provided in Supplementary Table S1). Two blank controls and five repeated samples were assigned into each 384-well format for quality control. The genotyping results were determined by the allelic discrimination mode of the SDS 2.3 software package (Applied Biosystems, Foster City, CA, USA), and a 100% concordant was achieved.
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