Sequence specific primers

Manufactured by Qiagen

Sequence specific primers are short, synthetic DNA molecules designed to bind to a specific target sequence within a longer DNA molecule. They are used as tools in various molecular biology techniques, such as polymerase chain reaction (PCR) and DNA sequencing, to selectively amplify or detect specific regions of a DNA sample.

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Lab products found in correlation

Steponeplus pcr system, by Thermo Fisher Scientific (3 mentions) Simplechip enzymatic chromatic ip kit, by Cell Signaling Technology (2 mentions) Trizol, by Thermo Fisher Scientific (2 mentions) C1000 thermal cycler, by Bio-Rad (1 mentions) Sybr green pcr kit, by Qiagen (1 mentions) Miscript reverse transcription kit, by Qiagen (1 mentions) Cdna synthesis kit, by Thermo Fisher Scientific (1 mentions) Miscript sybr green pcr kit, by Qiagen (1 mentions)

4 protocols using sequence specific primers

Quantitative Analysis of Drug Resistance Genes

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Total RNA was extracted from harvested cells with TRIzol (Thermo Fisher Scientific). Briefly, for the detection of Bcl-2, MRP3, MRP7, and P-glycoprotein, 1 µg of total RNA per sample was converted to cDNA using a cDNA Synthesis Kit (Thermo Fisher Scientific). The cDNAs were amplified and detected using a SYBR Green PCR kit (Qiagen). GAPDH was used as an endogenous control. For detection of the mRNA, cDNA products were synthesized using the miScript Reverse Transcription Kit (Qiagen). Sequence-specific primers targeting Bcl-2, MRP3, MRP7, P-glycoprotein, or the endogenous control U6 were purchased from Qiagen (Table 1). Quantitative reverse-transcription PCR (qRT-PCR) was performed using miScript SYBR Green PCR kit (Qiagen). All reactions were run in triplicate on a Bio-Rad C1000 thermal cycler (Bio-Rad). mRNA expression fold changes were calculated according to the 2^−ΔΔCT method.

Wu Y., Liu X., Qin Z., Hu L, & Wang X. (2018). Low-frequency ultrasound enhances chemotherapy sensitivity and induces autophagy in PTX-resistant PC-3 cells via the endoplasmic reticulum stress-mediated PI3K/Akt/mTOR signaling pathway. OncoTargets and therapy, 11, 5621-5630.

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ChIP Analysis of SREBP Binding to Bace1

Cited 1 time

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ChIP analysis was performed to evaluate the extent of SREBP1 and SREBP2 binding to the SRE in the mouse Bace1 promoter region using “SimpleChIP^™ Enzymatic Chromatic IP kit” from Cell Signaling (Boston, MA) following manufacturer’s instructions and as described earlier [31 (link)]. The relative abundance of the SREBP1- and SREBP2-antibody precipitated chromatin containing the SRE binding site in the mouse Bace1 promoter region was determined by qPCR using sequence specific primers (Qiagen Inc. Valencia, CA) (Table 5). The amplification was performed using the “StepOnePlus” PCR System (ABI, Foster City, CA). The fold enrichment of the bound - SREBP1 and SREBP2 in the mouse Bace1 promoter region was calculated using the ΔΔC_T method which normalizes ChIP C_T values of each sample to the % input and background. The data was further normalized and expressed as fold-change compared to control.

Marwarha G., Claycombe-Larson K., Lund J, & Ghribi O. (2018). Palmitate-induced SREBP1 expression and activation underlies the increased BACE 1 activity and Amyloid beta genesis. Molecular neurobiology, 56(7), 5256-5269.

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ChIP-qPCR Analysis of C/EBPα Binding

Cited 4 times

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ChIP analysis was performed to evaluate the extent of C/EBPα binding to the DNA elements in the leptin and IGF1 promoter region using “SimpleChIP^™ Enzymatic Chromatic IP kit” from Cell Signaling (Boston, MA) following manufacturer’s instructions as described earlier [7 (link), 10 (link), 11 (link), 39 (link)]. The relative abundance of the C/EBPα antibody precipitated chromatin containing the C/EBPα binding site in the leptin and IGF1 promoter region was determined by qPCR using sequence specific primers (Qiagen Inc. (Valencia, CA). The list of primers used for the ChIP analyses is presented in Table 5. The amplification was performed using the “StepOnePlus” PCR System (ABI, Foster City, CA). The fold enrichment of the bound C/EBPα in the leptin and IGF1 promoter region was calculated using the ΔΔC_t method which normalizes ChIP C_t values of each sample to the % input and background.

Marwarha G., Claycomb K., Schommer J., Collins D, & Ghribi O. (2016). Palmitate-induced Endoplasmic Reticulum stress and subsequent C/EBPα Homologous Protein activation attenuates leptin and Insulin-like Growth Factor 1 expression in the brain. Cellular signalling, 28(11), 1789-1805.

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Quantitative Analysis of p65 Binding to BACE1 Promoter

Cited 2 times

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ChIP analysis was performed to evaluate the extent of p65 binding to the NF-κB binding elements in the BACE1 promoter region using “SimpleChIP^TM Enzymatic Chromatic IP kit” from Cell Signaling (Boston, MA) following manufacturer’s instructions and as described earlier (Marwarha et al. 2017b , Marwarha et al. 2017c , Marwarha et al. 2017a (link), Marwarha et al. 2017e (link)). The relative abundance of the p65 antibody precipitated chromatin containing the NF-κB binding site in the BACE1 promoter region was determined by qPCR using sequence specific primers (Qiagen Inc. (Valencia, CA) (Table 5). The amplification was performed using the “StepOnePlus” PCR System (ABI, Foster City, CA). The fold enrichment of the bound p65 in the BACE1 promoter region was calculated using the ΔΔC_T method which normalizes ChIP C_T values of each sample to the % input and background. The data was further normalized and expressed as fold-change compared to control.

Marwarha G., Schommer J., Lund J., Schommer T, & Ghribi O. (2018). Palmitate induced C/EBP homologous protein activation leads to NF-κB -mediated increase in BACE1 activity and Amyloid beta genesis. Journal of neurochemistry, 144(6), 761-779.

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