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Idt oligo analyzer 3

Manufactured by Integrated DNA Technologies
Sourced in United States

The IDT Oligo Analyzer 3.1 is a software tool designed to analyze and evaluate the properties of oligonucleotide sequences. It provides detailed information about the physicochemical characteristics of DNA or RNA oligonucleotides, including melting temperature, GC content, and potential secondary structures.

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2 protocols using idt oligo analyzer 3

1

Rapid LAMP Assay for Salmonella Detection

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Bst DNA polymerase (Large Fragment) was purchased from Vazyme Biotech Co., Ltd. (Nanjing, China). Nt.BstNBI, ScrFI, DraI, and agarose were obtained from New England Biolabs (Ipswich, MA, USA). Syto 9 was achieved from Thermo Fisher (Waltham, MA, USA). 4-(2-Hydroxyethyl) piperazine-1-ethanesulfonic acid (HEPES), hemin, dNTP mixture, and ABTS were all supplied by Sangon Biotech (Shanghai, China) Co., Ltd. LB agar and LB broth were offered by Beijing Land Bridge Technology Co., Ltd. (Beijing, China) 30% H2O2 was bought from Sigma-Aldrich, Inc. (Burlington, MA, USA).
The gene of invasion protein A (invA) was selected as the reference gene for amplification (GenBank accession no. NC_003197). Conventional LAMP primers were synthesized according to the previous report [32 (link)]. Inner primers incorporated with the recognition site (GAGTC) of nicking endonuclease, Nt.BstNBI, are termed as Nick-BIP and Nick-FIP. All the sequences were evaluated with IDT Oligo Analyzer 3.1 (Integrated DNA Technologies, Coralville, IA, USA). The oligonucleotides were synthesized by Sangon Biotech (Shanghai, China) Co., Ltd. Sequences used in this work are listed in Table S1, and the corresponding template sequence is displayed in Figure S1.
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2

Quantifying BAF Complex Subunit mRNA

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qRT-PCR was used to examine mRNA levels of the BAF complex subunits. Three intron-spanning PCR primer sequences pairs were obtained for each gene of interest using NCBI Primer-BLAST program (Ye et al., 2012 (link)). Primer sequences were assessed for dimerization potential using IDT Oligo Analyzer 3.1 (Integrated DNA Technologies, Coralville, IA) and gene specificity and localization assessed via UCSC genome browser (Kent et al., 2002 (link)) in-silico PCR tool. Primers were then tested in duplicates using 250ng of cDNA harvested from GD12.5 murine neural stem cells, and thermal stability curves were assessed for evidence of a single amplicon. Selected amplicons were verified by sequencing (Texas A&M University Gene Technologies Lab) and compared to GenBank reference sequences for the gene of interest. Primer sequences are indicated in Table 1. RNA from neurospheres was isolated using Nucleospin columns (Macherey-Nagel, Bethlehem, PA) and cDNA were synthesized using qScriptâ„¢ cDNA SuperMix (Qiagen).
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