Category: Services

NGS

ITS amplicon sequencing

ITS amplicon sequencing service provides mycobial community profiling. We sequence total DNA extracted from complex matrixes (such as stool, soil, food) to obtain the identification and the abundance of Yeasts and Fungi in the sample.

Schizosaccharomyces pombe NCYC 3092. Often used in yeast genetics laboratories this species is also known as the ‘fission yeast’ because of the way its vegetative cells divide (by fission rather than by budding).

Schizosaccharomyces pombe NCYC 3092

What we do

  • DNA amplification of the ITS2 or ITS1 region with White et al. primers; click here for detailed information on primer sequences.
  • Barcoding with Illumina index and multiplexing;
  • Sequencing on Illumina Miseq with 300 bp paired-end approach.

Additional services

  • DNA extraction starting from stool, foods (i.e. cheese, yogurt, fermented beverages, etc), soil (20 €/sample). Click here for more information on this service.
  • We can provide sterile tubes with preservative buffer for sample shipment at room temperature (5 €/tube).

Output (click on the analysis name to read more about its method and deliverables):
1) Basic Offer: delivery of raw reads in fastq format (about 50,000 reads);
2) Taxonomic Analysis: Basic Offer + reads quality filtering and taxonomic assignments with UNITE database and abundance calculation. An example of the output is available here.

Requirements

  • DNA concentration between 3 and 10 ng/ul (verified by means PCR with primers for fungi/yeasts: see how to check your genomic DNA); it is customer responsibility to send the DNA of interest only;
  • DNA volume between 30 and 100 ul provided in 0,2 mL strip-tubes or 96-wells plate with caps (depending on the number of samples);
  • In case of 96-wells plate, H11-H12 wells must be empty. Please complete the following file (Template.xls) with samples ID and send it by e-mail to nextgen@bmr-genomics.it.

Note:
We test the input DNA with a PCR using universal primers and Illumina-based protocol. Samples not yielding any PCR product will be considered as not-compliant, thus the customer can decide either to stop (paying 10 euros/sample for the PCR done) or to continue with the protocol (but we don’t guarantee any result).

Shipment suggestion: in order to avoid DNA degradation during prolonged storage and shipment we suggest to send the samples in refrigerated packages, at 4°C or -20°C. It is customer responsibility to send the samples by means the most appropriate mode.

Delivery time

Results are usually delivered in about 10 weeks from sample arrival, depending on the working queue and sample compliance to requirements.

Prices

Contact us for more info at nextgen@bmr-genomics.it,  at +39 049 0995752 or using the following form:


NGS

Target Enrichment ToolKit: from DNA to data mining

target_enrichment_720Target Enrichment (TE) approach allows to selectively capture genomic regions of interest from a DNA sample before sequencing. Focusing on a limited set of genes, TE is an effective tool to detect disease-causing variants providing greater depth of coverage for increased analytical sensitivity and specificity.

TE ToolKit is a comprehensive service designed to simplify and speed up the identification and interpretation of genetic variants.

What we do

  • design and optimization of custom panel
  • library preparation
  • sequencing and quality control
  • bioinformatic analysis
  • use of the proprietary software SNP-shot, a variant selection and annotation tool to customize your research, based on self-defined filters.
  • use of the proprietary software PickPrimer, a tool to quinckly design all primers for variant validation by Sanger sequencing

Note: if you are interested only in one or some phases of the service please contact us.

Requirements

  • sample: Human genomic DNA
  • quantity: 2 ug
  • concentration: 50 ng/ul in ultrapure water, no EDTA
  • quality: high molecular weight DNA (no smear in gel <2,5 Kb); OD 260/289>1,8
  • shipping: + 4 °C or dry ice if delivery times should be more than 24 hours.
  • sample number: 44 or 88

Note: for target enrichment experiments on different species please contact us.

What we need to know

To prepare our best service offer, we need to know:

  • organism
  • list of genes (including related isoforms) or genomic regions of interest (target 1 kb 5 Mb)
  • sample number
  • average coverage per sample

Note: for target size greater than 5 Mb please contact us.

 

 

 

 


NGS

16S Amplicon sequencing

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OTUs phylogenetic tree

16S amplicon sequencing service provides microbial community profiling. We sequence total DNA extracted from complex matrixes (such as stool, soil, food) to obtain the identification and the abundance of all bacteria in the sample.

What we do

  • DNA amplification with V1-V3 or V3-V4 (either for Bacteria or Bacteria and Archaea) hypervariable regions primers (we propose 3 alternative primer pairs, to be specified)
  • Barcoding with Illumina indexes and multiplexing
  • Sequencing on Illumina Miseq with 300 bp paired-end approach.
    Additional services
    • DNA extraction starting from stool, foods (i.e. cheese, yogurt, fermented beverages, etc), soil (20 €/sample). Click here for more information on this service.
    • We can provide sterile tubes with preservative buffer for sample shipment at room temperature (5 €/tube).

Output (click on the analysis name to read more about its method and deliverables):

Requirements

  • DNA concentration between 3 and 10 ng/ul (verified by means PCR with primers for 16S: see how to check your genomic DNA);
  • DNA volume between 30 and 100 ul provided in 0,2 mL strip-tubes or 96-wells plate with caps (depending on the number of samples).
  • In case of 96-wells plate, H11-H12 wells must be empty. Please complete the following file (Template.xls) with samples ID and send it by e-mail to nextgen@bmr-genomics.it

We test the input DNA with a PCR using universal primers and Illumina-based protocol. Samples not yielding any PCR product will be considered as not-compliant, thus the customer can decide either to stop (paying 10 euros/sample for the PCR done) or to continue with the protocol (but we don’t guarantee any result).

Shipment suggestion: in order to avoid DNA degradation during prolonged storage and shipment we suggest to send the samples in refrigerated packages, at 4°C or -20°C. It is customer responsibility to send the samples by means the most appropriate mode.

Delivery time

Results are usually delivered in about 10 weeks from sample arrival, depending on the working queue and sample compliance to requirements.

Price

Prices start from 24,90 € depending on  the type of analysis, the number of samples and the requested bioinformatic analysis.

Contact us

Existing customers

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  2. Order your analysis now!

NGS

Microbial genome sequencing

Sequencing a novel genome enables molecular studies, addressing exciting questions spanning from adaptation to pathogenesis.

Our de novo genome sequencing service is complete: we prepare the libraries, perform the sequencing on the robust Illumina platform, and we perform the assembly and preliminary annotation.

What we do

  • Whole genome shotgun library
  • Illumina MiSeq sequencing, 300 bp paired-end
  • Sequencing QC
  • De novo genome assembly (producing contigs)
  • Automatic gene prediction and annotation using PROKKA 1.11
  • Personal BLAST server [optional]

Requirements

  • 1.0 ug genomic DNA
  • 260/280 1.8-2.0
  • Intact DNA, agarose gel checked

Should you work with difficult samples, giving lower yields of total RNA, please contact us to arrange custom specifications.

What we deliver

You’ll receive:

  • The raw sequences, in FASTQ format
  • The contigs produced by the de novo assembly steps, in FASTA format
  • The tabular coordinates of predicted genes, from gene prediction
  • The genome annotation in both GFF and GBK (GeneBank) format

What we need to know

Before writing us for a quote, To prepare our best service offer, we need to know:

  1. Your experimental goal (what are you looking for). The “standard” approach gives good results for re-sequencing of known bacteria and to produce a draft for novel genomes. If you are looking for genes or genome rearrangements we can propose scaffolding and finishing steps.
  2. If there are closely related genomes sequenced, and/or if you are resequencing a strain of well known bacteria
  3. The estimated genome size (in Mb)
  4. The number of organisms you wish to sequence.

Prices

Contact us for more info at nextgen@bmr-genomics.it,  at +39 049 0995752 or using the following form:

 


NGS

RNA-Seq for differential expression

RNA-Seq is a powerful technique to investigate the transcriptome. While RNA-Seq can be used for several applications, here we describe the differential expression service we provide using Illumina NextSeq 500.

What we do

  • mRNA enrichment (either via polyA+ or rRNA depletion)
  • library preparation
  • Illumina Sequencing
  • Sequencing QC (Basic analysis)

Optional Bioinformatics:

  • Analysis level 1: alignment and count
    • alignment against reference genome
    • raw gene counts
  • Analysis level 2: differential expression
    • differentially expressed genes analysis with edgeR

Requirements

  • 4.0 ug total RNA
  • RIN > 7

Should you work with difficult samples, giving lower yields of total RNA, please contact us to arrange custom specifications.

What we need to know

To prepare our best service offer, we need to know:

  1. Organism (which genome and annotation release to use, we usually provide the latest ENSEMBL annotation)
  2. Number of experimental conditions and biological replicates (we recommend to prepare at least 3 biological replicates for each condition)
  3. Number of reads per sample requested (we recommend a 15 to 40 million reads per sample, but according to your experimental set up this might change)
  4. Sequencing format (for differential expression for well known genomes we recommend 1x75bp, while for less known genomes or in case you are interested in alternative splicing detection we recommend 2×75 bp)
  5. Experimental set up: which conditions are to be compared (e.g.: control vs day1, control vs day2 and day1 vs day2)

Results

Click HERE to see an example of the results produced.

For more info or other options not included in the list write to nextgen@bmr-genomics.it, call us +39 049 0995752 (lab NGS) or fill the following form: