16S rDNA Metagenome Sequencing Service
16S rDNA Metagenome sequencing allows powerful insight into the composition of mixed microbial communities, enabling researchers to explore environmental samples and microbiome samples to a much deeper level than possible before. abm’s 16S metagenome sequencing service creates Illumina compatible libraries containing both the V3 and V4 hypervariable regions in the gene, but can easily be modified to examine different regions or different genes such as 18S and ITS. With multiplexing capabilities, up to 108 metagenome samples can be sequenced on a single MiSeq run.
abm is an Illumina Certified Service Provider, dedicated to ensuring the delivery of the highest-quality data available for genetic analysis applications.
"NGS from abm was always willing to advise me and agree with me to choose the best option for my experiments, something that not all companies do.
For this reason, I want to thank you for the vocation of service and how devoted you are to your customers, that is the best way to leave a seal on your customers, therefore you will always be my first option."
Service Details
Core Services
| PAIRED-END SEQUENCING | No.Samples | CAT. NO. | Unit Price |
|---|---|---|---|
| 16S rDNA | |||
| 16S rDNA Metagenomics Sequencing (Low throughput) | 1-49 | IA20100 | Inquire |
| 16S rDNA Metagenomics Sequencing (Medium throughput) | 50-79 | IA20200 | Inquire |
| 16S rDNA Metagenomics Sequencing (High throughput) | >80 | IA20300 | Inquire |
| Custom 16S Amplicon Primers Customer must provide published/validated primer sequence |
1 primer set | IA20001 | Inquire |
| 18S rDNA | |||
| 18S rDNA Metagenomics Sequencing (Low throughput) | 1-49 | IA20110 | Inquire |
| 18S rDNA Metagenomics Sequencing (Medium throughput) | 50-79 | IA20210 | Inquire |
| 18S rDNA Metagenomics Sequencing (High throughput) | >80 | IA20310 | Inquire |
| Custom 18S Amplicon Primers Customer must provide published/validated primer sequence |
1 primer set | IA20002 | Inquire |
| ITS rDNA | |||
| ITS rDNA Metagenomics Sequencing (Low throughput) | 1-49 | IA20120 | Inquire |
| ITS rDNA Metagenomics Sequencing (Medium throughput) | 50-79 | IA20220 | Inquire |
| ITS rDNA Metagenomics Sequencing (High throughput) | >80 | IA20320 | Inquire |
| Custom ITS Amplicon Primers Customer must provide published/validated primer sequence |
1 primer set | IA20003 | Inquire |
Bioinformatics Services
| SERVICE NAME | UNIT | CAT. NO. | UNIT PRICE |
|---|---|---|---|
| Standard Metagenome Analysis •Contig Assembly •OTU clustering and classification •Alpha diversity and Beta diversity analyses If multiple analyses are required, please specify. |
1 Sample | IB00021 | $38.00 |
Additional Services
| SERVICE NAME | UNIT | CAT. NO. | Unit Price |
|---|---|---|---|
| Sample and Library QC | 1 Sample | IR18001 | $60.00 |
| Data Storage (per additional 3 months) | IS10001 | $150.00 | |
| Hard Drive of NGS Results | 1 Hard Drive | IS10003 | Inquire |
Key Features for abm's Metagenome Sequencing Service
| Sequencing Platform | Illumina MiSeq |
|---|---|
| Sequencing Scale | Targeted: around 50,000 reads per sample (on average) |
| Starting Material | 50-100ng of metagenomeDNA |
| Sequencing Type | 2x250bp PE (standard) 2x300bp PE |
| Bioinformatics Analyses | Standard Metagenome Analysis |
| Turn-around Time | About 4-6 weeks from passing sample QC |
| Data Storage | 3 months |
abm offers exploratory bioinformatics analyses for metagenome samples from OTU classification to alpha/beta diversity analyses to facilitate your next discovery. See our sample report for more details.
Project Design/Advice Assistance
All of abm's sequencing services are performed by a group of specially trained and experienced scientists partaking in a streamlined workflow. Please contact our technical support team with details of your project requirements at [email protected] and our technical support team will be happy to work with you on confirming the details of your NGS order.
Confidentiality and Service Policy
All customer information is held in strict confidence. All materials and information sent to us and the products produced by us for the order are the property of the customer and will be returned to the customer or discarded in a confidential manner. We only archive customer materials when instructed to.
Our goal is always to deliver high-quality useful data to aid you in your research. We perform extensive maintenance and quality assurance on our equipment and strict quality control of samples throughout the sequencing process. However, next-generation sequencing by nature does not always deliver equally robust results due to a variety of factors, such as the variability inherent in the library preparation process, the biochemistry that takes place during sequencing and the quality of samples that we receive. We will make every effort to deliver the number of reads that are listed, although it is not possible to guarantee that those targets will always be achieved. The actual number of reads passing filter may vary by up to 10% from the listed target. Studies by various institutes have shown that there is minimal difference in coverage for 10% variation in reads past 5-10 million total reads.
All services are for research use only.
Our goal is always to deliver high-quality useful data to aid you in your research. We perform extensive maintenance and quality assurance on our equipment and strict quality control of samples throughout the sequencing process. However, next-generation sequencing by nature does not always deliver equally robust results due to a variety of factors, such as the variability inherent in the library preparation process, the biochemistry that takes place during sequencing and the quality of samples that we receive. We will make every effort to deliver the number of reads that are listed, although it is not possible to guarantee that those targets will always be achieved. The actual number of reads passing filter may vary by up to 10% from the listed target. Studies by various institutes have shown that there is minimal difference in coverage for 10% variation in reads past 5-10 million total reads.
All services are for research use only.
Related Products
FAQs
| Is your company certified as a service provider for Illumina Sequencing? |
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Yes, we are a certified Illumina service provider.
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| What kind of analysis software do you use for sequence analysis? |
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The Illumina sequencers come with the integrated software that can perform the regular bioinformatics analysis functions. In addition, we have extensive experience with other open access software such as Galaxy, Adnuril, BioBike, etc. In other words, we are willing to perform additional bioinformatics analysis with different software and tools to satisfy a variety of demands from our customers.
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| What kind of QC methods do you adopt for the customer's sample(s)? |
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We will perform QC on your Total RNA samples prior to sequencing them, using the Agilent Bioanalyzer (industry standard) to determine the RNA Integrity Number (RIN). If the RIN is lower than 8, we consider these samples as having failed QC. If the samples do not pass QC, we will ask you to send us new samples. If we do not receive new samples, thereby cancelling the sequencing order, there will be a QC fee of $50/sample. This fee will be waived if you choose to continue with the sequencing order. A strict positive and negative control will be applied to this QC process. The library QC will also be performed using the Agilent Bioanalyzer to determine library size and purity. Also, prior to loading the libraries on the sequencer, we perform qPCR quantification. The cost for this is included in the sequencing service. For the QC of the final data from our sequencing service, the integrated software will generally do the job and provide adequate QC information, however, we can also provide additional QC data such as FASTQC upon request. The data we output will pass our Q30 filter, which means that the error rate in base calls is less than 1 in 1000, or 0.1%. We will get a percentage at the end of the run which states the percentage of bases that have a Q score > 30, and this percentage is usually ≥85%.
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| What is the lead time for your WGS, WES, and RNA-Seq services? |
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Our sequencing lead times depend on workload, but are typically 2-4 weeks for sequencing data + 2-3 weeks for standard analysis. Please inquire for lead times for more detailed analysis.
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Citations
| 01 | Barclay, R. A. et al. "Exosomes from uninfected cells activate transcription of latent HIV-1." J. Biol. Chem 292(28):11682-11701 (2017). DOI: 10.1074/jbc.A117.793521. Application: RNA-Seq. |
| 02 | Ee, LS et al. "An Embryonic Stem Cell-Specific NuRD Complex Functions through Interaction with WDR5." Stem Cell Rep 8(6):1488-1496 (2017). DOI: 10.1016/j.stemcr.2017.04.020. Application: RNA-Seq. |
| 03 | Acharya, D et al. "KAT-Independent Gene Regulation by Tip60 Promotes ESC Self-Renewal but Not Pluripotency." Cell Rep 19(4):671-679 (2017). DOI: 10.1016/j.celrep.2017.04.001 .Application: RNA-Seq. |
| 04 | Goudarzi, R et al. "Effects of Arthrocen, an avocado/soy unsaponifiables agent, on inflammatory mediators and gene expression in human chondrocytes." FEBS Open Bio 7(2):187-194 (2017). DOI: 10.1002/2211-5463.12176. Application: RNA-Seq. |
| 05 | Taylor, J.F. et al. "In Vitro Effects of Arthrocen, an Avocado/Soy Unsaponifiables Agent, on Inflammation and Global Gene expression in Human Monocytes." IJC 9(4):31-39 (2017). DOI: 10.5539/ijc.v9n4p31. Application: RNA-Seq. |
| 06 | Alam, S.B. and Rochon, D. "Cucumber Necrosis Virus Recruits Cellular Heat Shock Protein 70 Homologs at Several Stages of Infection." J Virol 90 (7):3302-3317 (2016). DOI: 10.1128/JVI.02833-15. PubMed: 26719261. Application: RNA-Seq. |
| 07 | Ghoshala, K et al. "Encapsidation of Host RNAs by Cucumber Necrosis Virus Coat Protein during both Agroinfiltration and Infection." J Virol 89(21):10748-61 (2015). DOI: 10.1128/JVI.01466-15. PubMed: 26269190. Application: Next Generation Sequencing. |
| 08 | Nakamura, S et al. "Novel roles for LIX1L in promoting cancer cell proliferation through ROS1-mediated LIX1L phosphorylation." Sci Rep 5:13474: (2015). DOI: 10.1038/srep13474. PubMed: 26310847. Application: Next Generation Sequencing. |