PCR Plus Sequencing CRISPR Analysis
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This service includes PCR optimization, amplicon production and purification, TA cloning (if needed), and Sanger sequencing to confirm a mutation or determine the genotype and specific allelic events generated by your CRISPR editing.
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We accept purified gDNA, cell pellets, blood, tissue, buccal swabs, saliva, and FFPE samples. Please inquire about additional sample types in the comments section of your order form or by sending an email to molgen@azenta.com.
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Yes, we can design assays to target your region of interest. We request submission of the accession number or chromosome position, genome build, and the name of the gene or SNP ID of interest. You may also provide a reference sequence in text format with your target(s) of interest highlighted, and 200 bp of flanking sequence on either side of the target(s).
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Yes, GENEWIZ can accept previously designed assays. There will be an assay optimization fee to ensure that the assay is robust and functional in our lab. Primers can either be submitted with the samples, or the sequence information can be submitted and we will order the corresponding primers.
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Yes, we can process assays that are longer than 500 bp. Additional charges apply and will vary depending on the size of the target region. Typically paired-end sequencing is included in the sample processing. If additional coverage for the entire amplicon is needed, please indicate this in the comments section of the order form.
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If you anticipate either large or complex INDELS or expect that your mutation has a low frequency of occurrence, you can choose the TA cloning option up front. Alternatively, our team can perform the PCR and Sanger sequencing and, depending on the outcome of the analysis, you can choose to add the TA cloning service to a specific subsets of samples.
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Deliverables include the original sequencing results in chromatogram format (.ab1 files) as well as the sequence files (.seq files).
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Standard analysis will include wild type, heterozygous, and complex INDEL calls made at the nucleotide level. Please note that in order to resolve complex INDELs, we will need to perform TA cloning.
Quantitative PCR (qPCR)
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Quantitative PCR (qPCR or real-time PCR) and RT-qPCR (reverse transcription quantitative PCR) methods measure the abundance of specified nucleic acid sequences in a sample. qPCR combines PCR amplification with a fluorescent probe that reacts to the presence of a specific DNA or RNA sequence. This simple approach is a powerful investigational tool with broad applications in healthcare, research, quality assurance, and many other fields.
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Our expert scientists can assist at virtually any stage of your qPCR or RT-qPCR project. We accept fresh frozen tissue, blood, buccal swabs, cell pellets, purified RNA, cDNA, or gDNA as starting material. Please see our sample submission guidelines for details on sample types, minimum starting materials, and recommended QC parameters.
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We offer gene expression, genotyping, copy number variation (CNV), and viral titer qPCR services. We also accommodate custom assays, such as multiplexed qPCR. Contact us at molgen@azenta.com for more information on custom qPCR approaches.
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We suggest the use of Taq-Man chemistry and probes whenever possible. We also accept custom probes for SYBR-based qPCR projects.
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Our team can design and optimize qPCR assays on a case-by-case basis. Please contact us at molgen@azenta.com to find out more about our custom assay design services.
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We are flexible to the needs of your unique experiment. However, for gene expression approaches, we recommend the inclusion of at least two (2) normalization probes, also known as ‘house-keeping’ genes, for each sample. For genotyping approaches, we recommend probe validation of 3 or more known control samples for each investigated allele.
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Log in to or register for your GENEWIZ account at Molecular Genetics (PCR + Sanger) > qPCR. Fill in the required information and submit the quote request form.
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For all questions in the form, please select the option that best matches your project requirements and specify your exact needs in the comments section.
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Please view our detailed sample submission guidelines and consult the best practices checklist before submitting your samples.
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Our team can work with BSL1 and some BSL2 specimens, so depending on the type of virus or infectious material in your samples, we may be able to accept them. If you will be submitting samples that contain viral/infectious materials, please mention it in the comments section of the quote request form, or contact us via email at molgen@azenta.com or call 877-436-3949, ext. 3350.
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Our team is composed of expert scientists who can help you optimize your project design and provide consultation. Please contact us via email at molgen@azenta.com or call 877-436-3949, ext. 3350 to set up a technical consultation session with one of our team members.
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We can accept CLIA or GLP-grade qPCR projects on a case-by-case basis. Please contact our CLIA team via email at CLIA@azenta.com or call 877-436-3949, ext. 1 if you’re interested in clinical-grade services.
Digital PCR (dPCR)
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Digital PCR (dPCR) is a new method of nucleic acid quantification that partitions a sample into thousands of nanoliter-sized droplets or wells, each of which undergoes PCR amplification. The resulting data can be used to determine the absolute quantity of the target nucleic acid sequence in the sample.
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qPCR amplifies a target sequence in the presence of a fluorescent dye until it reaches detectable levels. dPCR partitions these reactions into thousands of droplets or wells and each partition is amplified and measured independently. This enables more precise quantification of the target nucleic acid in a sample, down to single-copy resolution.
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ddPCR involves partitioning a sample into thousands of water-in-oil droplets using a specialized droplet generator. Chip-based dPCR, on the other hand, involves partitioning a sample into thousands of wells on a microfluidic chip. Both techniques have similar principles, but the methods of partitioning differ. One advantage of digital PCR methods is that the number of available partitions does not vary between reactions in the same experiment.
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Digital PCR is a targeted approach that quantifies the absolute amount of a known DNA sequence in a sample, whereas NGS is an unbiased approach that sequences millions of DNA fragments simultaneously to identify and quantify a sample.
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dPCR offers increased precision, reproducibility, and sensitivity over qPCR, RT-qPCR, and other available nucleic acid quantitation methods. Digital PCR is also more robust in the presence of PCR inhibitors, allowing even challenging samples to be quantified effectively. dPCR can also be used to detect rare targets in complex samples, such as low-abundance transcripts in total RNA.
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dPCR has broad applications in research and development, clinical diagnostics, biotechnology, and beyond. dPCR excels in copy number variation (CNV), detection of low-level mutations or rare transcripts, and is used in the evaluation of viral titer as well as quantification of viral vector copy number (VCN) of treated cells for AAV, lentivirus, and retrovirus in clinical research.
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Experimental design and expertise in dPCR quantitation are the most pivotal factors for success in any dPCR experiment. Other key considerations include the quality and quantity of starting material, reaction conditions, and primer/probe design.
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Absolute quantification determines the exact number of copies of a target nucleic acid in a sample, whereas relative quantification measures the fold change in target nucleic acid expression between two samples.
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Our expert scientists can assist at virtually any stage of your dPCR project. We accept fresh frozen tissue, blood, buccal swabs, cell pellets, purified RNA, cDNA, or gDNA as starting material. Please see our sample submission guidelines for details on sample types, minimum starting materials, and recommended QC parameters.
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Our team can design and optimize dPCR assays. Please contact molgen@azenta.com to find out more about our custom design services.
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By working with Azenta, researchers and companies can benefit from customized and optimized dPCR solutions that can improve accuracy, sensitivity, and efficiency, while reducing variability and development time.
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Our team is composed of expert scientists who can discuss your project goals and determine how Azenta can best assist you with design and customization services for dPCR. Please contact us via email at molgen@azenta.com to set up a technical consultation session.
SNP/Mutation Analysis
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SNP/mutation analysis is a PCR and Sanger sequencing technique for analyzing single nucleotide polymorphisms (SNPs) and mutations in genomic DNA.
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We accept purified gDNA, cell pellets, fresh/frozen tissue samples, FFPE samples, blood, buccal swabs, saliva, and yeast and bacterial colonies. Please inquire about other sample types by adding a comment in the “comments section” of your order form or by sending an email to molgen@azenta.com.
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Yes, we can design assays to target your nucleotide region of interest. We request submission of the accession number or chromosome position, genome build, and the name of the gene or SNP ID of interest. You may also provide a reference sequence in text format with your target(s) of interest highlighted, and 200 bp of flanking sequence on either side of the target(s).
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Yes, you can send us assays originally designed in your lab. We will charge an assay optimization fee to ensure that the assay is robust and functional in our lab. You can either supply custom primers with your sample or give us the sequencing information and we will synthesize the primers.
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Yes, we offer internally validated predeveloped assays for a variety of genomic targets. These assays offer a low-cost and quick solution for sequencing common targets in the human genome. For a list of our predeveloped assays, please click here. If you do not see your target offered, please email us at molgen@azenta.com and our team will be happy to accommodate your research needs.
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Amplicons are targeted to be 400-500 bp for standard samples and 150-250 bp for FFPE samples. However, we can design larger PCR amplicons for an additional cost. This may vary depending on the complexity of the region of interest for a particular project.
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The fixation procedure tends to introduce some degradation into formalin-fixed paraffin embedded (FFPE) samples. With FFPE samples, smaller amplicons are required to maximize success rates in the PCR assay because it is much more difficult to analyze degraded DNA containing large amplicons.
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Yes, we can but that will incur additional charges according to the size of the target region. Although standard sample processing involves end-sequencing, if you need additional coverage for the entire amplicon, please make the request in the “comments section” of the order form.
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You will receive the original sequencing results in a chromatogram (.ab1 files) and the sequence files (.seq files).
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Standard analysis includes mutation calls made at the nucleotide level. You may request “custom analysis” including translated amino acid calls for an additional fee.
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We will process the samples once with the expectation that 80% of the sequences will be deemed “clean.” In case we do not attain that threshold, we will automatically repeat the assay free of charge.
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If it is necessary, we will perform a single repetition of the PCR and sequencing reactions in order to achieve cleaner traces.
16S rRNA Gene Sequencing
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This is a PCR and Sanger sequencing technique for identifying bacterial strains through the analysis of the 16S ribosomal RNA (16S rRNA) gene. It contains highly conserved regions between different species of bacteria, and this allows for targeting via PCR. After data analysis, the differences between species identified through Sanger sequencing, allows you to distinguish between individual samples.
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We accept clonal colonies on agar plates, glycerol stocks or purified gDNA samples.
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We use a Universal Primer set for the assay but the actual sequences are proprietary.
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The primers target the V1 to the V9 regions of the 16S rRNA gene.
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The PCR assay generates a 1.5kb PCR product.
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No, this service is for clonal samples that are not from a mixed population.
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You will receive the original sequencing results in a chromatogram (.ab1 files) and the sequence files (.seq files).
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No, but you can use the raw data we provide to identify bacterial strains.
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No, this service is not applicable to yeast.
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Although we have processed 18S assays submitted by our customers, currently we do not offer a universal 18S in-house assay.
ITS Sequencing
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ITS, or internal transcribed spacer, refers to spacer DNA found between the small subunit ribosomal RNA and large subunit ribosomal RNA genes.
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The ITS region is the most commonly sequenced DNA region for identification of fungi (yeast and mold). This PCR and Sanger sequencing technique analyzes the ITS spacer regions that are highly conserved between different species of fungi, allowing researchers to distinguish between their individual samples once the data is analyzed.
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We accept clonal colonies on agar plates, glycerol stocks or purified gDNA.
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GENEWIZ utilizes proprietary primers designed to target the ITS regions.
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The primers target the ITS1 and ITS2 regions found between the 18S and 28S rRNA genes in fungi.
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The PCR assay generates a ~600-800 bp PCR product.
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No, this service line is only intended for clonal samples that are not from a heterogeneous population.
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You will receive the original sequencing results in a chromatogram (.ab1 files) and sequence (.seq files) format.
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No, but you can use the raw data we provide to identify fungal strains.
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GENEWIZ offers 16S rRNA gene sequencing that can be utilized for bacterial samples.
cDNA Verification
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We accept RNA, cDNA, cell pellets, fresh/frozen tissue samples, FFPE samples, blood, and viral particles. Please inquire about other sample types by adding a comment in the “comments section” or by sending an email pm@azenta.com.
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Yes, we can design assays to target your region of interest. We request submission of information pertaining to the transcript(s) of interest per gene. If multiple transcripts need to be targeted, please include that information in your quote request and the project will be designed accordingly.
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Yes, we can design assays to amplify endogenous and recombinant targets. For endogenous targets, we request submission of information pertaining to the transcript(s) of interest per gene. For recombinant targets, please submit the reference sequence for the target of interest, including any flanking sequence surrounding the target, at least 100 bp 5’ and 3’ of the target region, if available.
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Yes, previously designed assays can be sent to the lab. The lab will need to ensure that the assay is robust and functional in our lab. Primers can either be submitted with the samples or the primer sequence information can be submitted and we will order the corresponding primers.
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We will design the primers based on the 5’ and 3’ end of the reference sequence you submit. Please note that the primers will mask the natural sequence on these ends of the reference sequence.
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No, we do not offer genome walking services. We can verify that the region of interest exists, but we will not go beyond that to identify the gene location with this method.
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Yes, we include two controls (i.e., no reverse transcriptase and no template controls) during the reverse transcription reaction.
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We will send you the original sequencing results in chromatogram format (.ab1 files), the sequence files per trace (.seq files), a consensus file of the aligned traces (.seq), and an alignment file of the consensus sequence against the reference sequence (.pdf).
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A custom report includes the primers used in the project and a consensus sequence for the region of interest. Any discrepancies between the sequence traces and the reference sequence will be highlighted within the report.
gDNA Verification
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gDNA verification is a PCR and Sanger sequencing technique for confirming longer stretches of a sequence in a gDNA sample. The gDNA is used as template for PCR in order to target the region of interest. Sanger sequencing is then used to confirm the sequences in the target region. Typically, this application is used to confirm changes made during cell line engineering experiments.
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We accept gDNA, cell pellets, fresh/frozen tissue samples, FFPE samples, blood, and viral particles. Please inquire about other sample types by adding a comment in the “comments section” or by sending an email to pm@azenta.com.
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Yes, we can design assays to target your region of interest. We request submission of information pertaining to the particular gene of interest or region of gDNA. If an engineered sequence needs to be targeted, please submit this sequence information in your quote request and the project will be designed accordingly.
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Yes, we can design assays to amplify recombinant targets. For recombinant targets, please submit the reference sequence for the target of interest including flanking sequence surrounding the target, at least 100 bp 5’ and 3’ of the target region, if available.
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Yes, previously designed assays can be sent to the lab. The lab will need to ensure that the assay is robust and functional in our lab. Primers can either be submitted with the samples or the primer sequence information can be submitted and we will order the corresponding primers.
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We will design the primers based on the 5’ and 3’ end of the reference sequence you submit. Please note that the primers will mask the natural sequence on these ends of the reference sequence.
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No, we do not offer genome walking services. We can verify that the region of interest exists, but we will not go beyond that to identify the gene location with this method.
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We will send you the original sequencing results in chromatogram format (.ab1 files), the sequence files per trace (.seq files), a consensus file of the aligned traces (.seq), and an alignment file of the consensus sequence against the reference sequence (.pdf).
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A custom report includes the primers used in the project, consensus sequence for the region of interest, and a highlight of any discrepancies between the sequence traces and the reference sequence.
Have a specific question?
Email | Phone 1-877-GENEWIZ (436-3949), Ext. 3350
Plasmid Prep FAQs
Service Options
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Our plasmid prep includes a standard-scale service with mini to giga scale preps, and a targeted yield service to deliver specific quantities of transfection-grade DNA. We also offer 96-well-mini-preps, custom large-scale preps, and AAV plasmid preps for your specific project needs. Plasmid prep can also be ordered using bacterial colonies or glycerol stocks from a Sanger sequencing order.
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We offer a wide variety of analysis options with your plasmid prep order including DNA sequencing, restriction digest analysis, sterility testing, and much more.
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We have proven a steadfast commitment to superior service over the last two decades, becoming a global leader in genomics services. With plasmid DNA preparation, we offer rapid turnaround times starting at just 2 business days, convenient online ordering, and a strict QC process with a wide range of analysis options to ensure high-quality plasmids.
Completing the Order Form
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The table below provides guidance on selecting the appropriate cell line based on factors such as expression system, target protein, and downstream applications.
| Strain | Best for |
| DH5alpha | Regular cloning and storage, uptake of large plasmids |
| Top10 | Regular cloning and storage |
| Stable | Lentiviral and retroviral plasmids, plasmids prone to rearrangement |
| AAV | Proprietary cell strain used for our AAV-ITR plasmid production services, designed to maximize ITR stability |
Sample Submission
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- Purified DNA: At least 5 µL of DNA at 200 ng/µL (minimum 100 ng). Additional charge applies.
- Agar plate: Fresh (<3 days old) plate with single, well isolated colonies. Customer may indicate the colony (or colonies) to use, if desired.
- Glycerol stock or media sample: At least 200 µL. We can streak colonies (additional charges apply) for isolation prior to starting the liquid culture upon request.
- Cell pellet: Ship frozen on dry ice (direct to us via overnight carrier), with an indication of the culture volume, media used, OD600 at harvest, and cell pellet mass.
- DNA on filter paper: This format is discouraged – please send as purified, wet DNA in a sealed tube via overnight shipping (or our courier, if available). Additional charge applies.
- Other samples: Please contact our Technical Support team to discuss custom requirements.
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We routinely stock Carbenicillin (Carb), Kanamycin, Chloramphenicol, Ampicillin, Tetracycline, Streptomycin, Spectinomycin, and Zeocin. We also supply Gentamycin, Hygromycin, Apramycin, and Erythromycins but do not keep them on hand, so some lead time will be necessary. An automatic upgrade of Ampicillin to Carbenicillin is included at no added charge. Other antibiotics may be submitted by the customer with their samples.
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Fresher is better; < 3days old with well isolated colonies. Older plates can be freshly streaked for isolation upon request. Please note that this will add to the order timeline.
Please use caution in shipping agar plates during the cold winter months. The agar media may freeze in transit, rendering the plate unusable. Glycerol stocks are recommended as a substitute format during this season.
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Our plasmid prep team accepts only BSL1 samples. Typical agar plates used for these strains, bearing well isolated colonies are usually acceptable.
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Our Plasmid DNA Preparation service is for plasmids in the 3-15 kb range. We do not currently offer BAC or cosmid preparation services.
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We do not currently offer BAC or cosmid preparation services. Plasmids requiring handling outside standard protocols are reviewed on a case-by-case basis. Additional charges may apply.
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Please send at least 10 µL for each sequencing reaction using that primer. The primer concentration should be 5 µM.
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Larger plasmids (>10 kb) and plasmids containing toxic or unstable sequences (such as long terminal repeats (LTR) found in viral expression vectors) are likely to produce better results when paired with cell lines engineered to maintain these difficult sequences.
We advise against using standard cloning strains for these plasmids, due to increased risk of lower yield and plasmid instability. We also suggest the selection of additional QC testing to verify unstable or toxic plasmids.
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Please contact our Project Management team at GS@azenta.com or 908.222.0711 ext. 3 with any questions or to discuss your project.
Turnaround Time and Troubleshooting
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Typical turnaround time is 2-4 business days, depending on the order options selected. Additional testing or repeats may extend the timeline.
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- Log into your account and view My Orders. From this main menu you can also see Order Status next to each individual tracking number.
- If additional help is needed, please contact our Project Management team at GS@azenta.com or 908.222.0711 ext. 3 with any questions or to discuss your project.
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Upon request, we will store a sample of your starting material or final DNA for up to one year at no additional charge, to facilitate subsequent ordering. Please be sure to request this storage in your order comments and include the order tracking number when reordering preps.
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Azenta Project Management stores a sample of your final DNA from a gene synthesis order for up to one year at no additional charge. To order preps from these projects, simply go to the gene synthesis results page, select the construct of interest in the checkbox, and click “submit prep order” to initiate an online plasmid prep order.
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Our internal quality monitoring will trigger the automatic repeat of a plasmid DNA preparation when the yield is below a critical threshold, depending on the anticipated copy number for the plasmid. Yield variance above this threshold could be due to a variety of factors and may be intrinsic to the sample provided.
Plasmid DNA preparation orders are processed by run. For low copy or other low yield plasmids, we recommend ordering a larger preparation scale or multiple preps, depending on the amount of final material required.
To discuss troubleshooting or custom process modifications, please contact our Project Management team at GS@azenta.com or 908.222.0711 ext. 3 with any questions or to discuss your project.
GLP-level Plasmid Preparation
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Our Quality System is developed in accordance with applicable FDA GLP regulations described in Title 21, Part 58 of the Code of Federal Regulations and EPA GLP regulations described in Title 40, Part 160 of the Code of Federal Regulations. We offer GLP services including GLP Plasmid Prep. For more details, please contact us at 877-436-3949, ext. 3350 or Regulatory@Azenta.com.
