The largest database of trusted experimental protocols

Custom made primers

Manufactured by Thermo Fisher Scientific
Sourced in Italy, United States, Canada

Custom made primers are short, synthetic DNA sequences designed to serve as the starting point for DNA amplification in various molecular biology techniques. They are created to target specific regions of interest within a DNA sequence, enabling researchers to selectively amplify and study those regions.

Automatically generated - may contain errors

6 protocols using custom made primers

1

Osteoclastic Differentiation and Gene Expression

Check if the same lab product or an alternative is used in the 5 most similar protocols
Total RNA from Raw264.7 cells treated as described above (Raw264.7 osteoclastic differentiation and co-culture paragraphs) was extracted using a PureLink™ RNA Micro Kit (Invitrogen™) and reverse-transcribed with a High Capacity cDNA Reverse Transcription Kit (Applied Biosystems™, Life Technologies - Italy) following the manufacturer’s instructions. Each cDNA sample was tested in duplicate. qRT-PCR analysis was performed by using the SYBR® Green Real-Time PCR Master Mix (Applied Biosisystems™). Custom made primers (Invitrogen™) employed are reported in Table 1. The mean threshold cycle was used for the calculation of relative expression using the 2-ΔΔCt method, against Gapdh as housekeeping gene and Raw264.7 control cultures (CTR – maintained in their growth medium) as calibrator [42 (link)].

InitrogenTM sequences employed for gene expression studies

GeneForward primer sequence (5′-3′)Reverse primer sequence (3′-5′)
GapdhCCCAGAAGACTGTGGATGGCAGATTGGGGGTAGGAACAC
Acp5GCGACCATTGTTAGCCACATACGCGTTGATGTCGCACAGAGGGAT
CtskGCGTTGTTCTTATTCCGAGCCAGCAGAGGTGTGTACTATG
Mmp9GCTGACTACGATAAGGACGGCAGCGGCCCTCAAAGATGAACGG
+ Open protocol
+ Expand
2

Quantitative Real-Time PCR Analysis

Check if the same lab product or an alternative is used in the 5 most similar protocols
Total RNA was extracted using a PureLink TM RNA Micro Kit (Invitrogen TM ) and reversetranscribed with a High Capacity cDNA Reverse Transcription Kit (Applied Biosystems TM , Life Technologies -EuroClone S.p.A, Pero-Milan, Italy) following the manufacturer's instructions. Each cDNA sample was tested in duplicate.
qRT-PCR analysis was performed by Light Cycler 2.0 Instrument (Roche Diagnostics) using the SYBR® Green Real-Time PCR Master Mix (Applied Biosisystems TM ), QuantiTect Primers (Qiagen Srl, Milan, Italy) and custom made primers (Invitrogen TM ) (see Tables 1 and2). The mean threshold cycle was used for the calculation of relative expression using the 2 - ΔΔCt method, against GAPDH as housekeeping gene (Livak and Schmittgen, 2001) . Results were expressed as relative fold changes calculated using untreated MSCGM samples as calibrators for each experimental time point.
+ Open protocol
+ Expand
3

Liver Gene Expression Analysis by RT-PCR

Check if the same lab product or an alternative is used in the 5 most similar protocols
RT-PCR and real-time RT-PCR were used to analyze the gene expression in the liver on day 7 after BDL surgery. Total RNA was extracted from mouse liver using the Total RNA Extraction Miniprep System (Viogene BioTek, New Taipei City, Taiwan). The whole extraction process was performed under RNase-free conditions in order to prevent RNA degradation. Custom made primers and TaqMan probe for employed genes amplification were purchased from Life Technologies. The relative expression of each gene was normalized to that of 18S ribosomal RNA using random primers.
+ Open protocol
+ Expand
4

RT-qPCR Analysis of LDHA Expression

Check if the same lab product or an alternative is used in the 5 most similar protocols
Total RNA was extracted by Trizol Reagent (Takara, Shiga, Japan) and the first strand synthesis kit (Takara, Shiga, Japan) was used for reverse‐transcription reaction to prepare cDNA samples. The quantitative real‐time PCR (qRT‐PCR) was conducted by SYBR Green reagents (Takara, Shiga, Japan) on LightCycler 480 real‐time PCR system (Roche Life Science, Basel, Switzerland). The expression of beta‐actin was used as internal control for the normalization of targeted genes’ expression. The custom‐made primers (Life Technologies, Carlsbad, CA, USA) for RT‐PCR analysis are as follows: LDHA (h, human) forward: CCCCAGAATAAGATTACAGTTGTTG, LDHA(h) reverse: GAGCAAGTTCATCTGCCAAGTC; LDHA(m, mouse) forward: CTGGCTCCAGTGTGTACGTC, and LDHA(m) reverse: TGGGTGGTTGGTTCCATCAT; β‐actin(h) forward: CTACGTCGCCCTGGACTTCGAGC; and β‐actin(h) reverse: GATGGAGCCGCCGATCCACACGG; and β‐actin(m) forward:  TGTCCACCTTCCAGCAGATGT, β‐actin(m) reverse: AGCTCAGTA ACAGTCCGCCTAG.
+ Open protocol
+ Expand
5

Molecular Techniques for Cell Analysis

Check if the same lab product or an alternative is used in the 5 most similar protocols
DMEM/F-12 growth medium, Glutamax, Hu IL-8 Cytoset ELISA kit, PureLink Genomic DNA mini kit, Quant-iT RNA BR assay kit, NuPAGE Novex 4–12% Bis-Tris gel, TRIzol reagent, DNAse1-RNAse-free (AM2222), Superscript III reverse transcriptase, RNAseOUT recombinant Ribonuclease inhibitor, dNTP, DTT, aprotinin, Lipofectamine, microAMp optical 384 well reaction plate, custom-made primers, and 1 kb plus DNA ladder were purchased from Life Technologies (Burlington, ON, Canada). Normocin was obtained from InvivoGen (San Diego, CA, USA). ATP, ADP, AMP, adenosine, ATP-γ-S, suramin, diadenosine pentaphosphate (Ap5A), malachite green, and random nonamers (R7647) were purchased from Sigma. Millex GP syringe-driven filter unit 0.22 µm and Immobilon-P membrane were from Millipore (Billerine, MA, USA). Hank's balanced salt solution (HBSS) with Ca2+ and Mg2+, Hepes, and antibiotic-antimycotic solutions was from Wisent (St. Bruno, QC, Canada). RNeasy mini kit and QuantiTect Reverse Transcription kit were from Qiagen (Mississauga, ON, Canada). Taq polymerase was obtained from New England Biolabs (Ipswich, MA, USA) and FastStart Universal SYBR Green Master (Rox) was from Roche (Mannheim, Germany).
+ Open protocol
+ Expand
6

Quantifying Gene Expression via qRT-PCR

Check if the same lab product or an alternative is used in the 5 most similar protocols
Total RNA was extracted, using the miRNeasy Plus Mini Kit (Qiagen, Hilden, Germany) manufacturer protocol. UGT1A1, 1A6, 1A9, and 2B7, expression levels were determined via qRT‐PCR using GAPDH as an endogenous control. RNA quantification and quality were assessed, using optical spectrometry ratios (260/280 and 260/230 nm); mRNA was reverse transcribed to cDNA using the iScript Reverse Transcription Kit (Bio‐Rad, Hercules, CA) and diluted to obtain 25 ng/mL final cDNA concentration. Here, qRT‐PCR was performed on an Applied Biosystems Quantum Studio Viia 7 system with iTaq Universal SYBR Green (Bio‐Rad) and custom made primers (Life Technologies). The thermocycler parameters were 95°C for 30 seconds, then 40 cycles consisting of 95°C for 15 seconds followed by an annealing temperature for 30 seconds. Primer sequences and annealing temperatures are provided in Table S1. The delta–‐delta CT method was applied to determine the relative expression of each gene for rifampin and vehicle‐treated cells as previously described.5 The fold change in gene expression is represented as the mean ± SEM of the biological replicates (n = 4).
+ Open protocol
+ Expand

About PubCompare

Our mission is to provide scientists with the largest repository of trustworthy protocols and intelligent analytical tools, thereby offering them extensive information to design robust protocols aimed at minimizing the risk of failures.

We believe that the most crucial aspect is to grant scientists access to a wide range of reliable sources and new useful tools that surpass human capabilities.

However, we trust in allowing scientists to determine how to construct their own protocols based on this information, as they are the experts in their field.

Ready to get started?

Sign up for free.
Registration takes 20 seconds.
Available from any computer
No download required

Sign up now

Revolutionizing how scientists
search and build protocols!