BMR Genomics

Welcome to our NGS website

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:

 

 

Tags: rna-seq