RNA-Seq

Technologies
HiSeq 2500
NextSeq500
Nucleic acids extraction
RNA-Seq

Full view of the extent and complexity of transcriptomes

 
We’ve been working with IGATech and we’re extremely satisfied. I would suggest IGATech to any group who wants more than a sequencing facility, rather looking for a research partner to be involved in each step of your projects, from experimental design to data analysis.

Raffaele Teperino, PhD
Head of Environmental Epigenetics
Helmoholtz Center, Munich (Germany)

 

The transcriptomics field has developed rapidly with the advent of NGS technologies. The amount of valuable information that can be obtained from RNA-Seq data is truly enormous. A single experiment allows for gene expression analysis, detection of alternative splicing events, rare or novel transcripts and gene fusions, discovery of SNPs, identification of non-coding RNAs and their targets and measurement of allele-specific expression. Constant technological improvements allow for robust analysis on a wide range of samples, including low-quantity, low-quality and FFPE samples, as well as single cell sequencing.

 

CUTTING-EDGE APPROACHES FOR CUTTING-EDGE EXPERIMENTS

We provide targeted depletion of unwanted transcripts, which results in a significant reduction in sequencing reads derived from cytoplasmic and mitochondrial rRNAs, globin, chloroplasts, housekeeping genes, or any other transcript species that may not be relevant to a study, for more efficient use of sequencing resources.

As a part of our standard procedure we prepare strand oriented RNA-seq “libraries” that maintain the information on which strand the original mRNA template is coming from allowing to accurately determine gene expression from overlapping genes, i.e. those that have at least partially overlapping genomic coordinates, but are transcribed from opposite strands.

 

We use tools for efficient cDNA generation from ultra-low inputs supporting research in areas previously hampered by low quantity limitations such as blood-borne biomarkers, cellular heterogeneity, and the study of single cell transcriptomics.

SINGLE CELL SEQUENCING

gene expression profiling of hundreds to millions of cells by 10x Chromium Technology

For the high-throughput single cell sequencing we use 10x Genomics Chromium System that permits to perform deep profiling of heterogeneous populations with digital gene expression on a cell-by-cell basis ensuring that biologically relevant signals of individual cells are not masked by bulk average measurements.

 

 

We perform a highly customizable Targeted RNA-Seq expression assays, which generate data equivalent to individual RT-PCR assays and offer an accurate and powerful method for validating gene expression arrays and RNA-Seq studies.

 

 

IMMUNE REPERTOIRE PROFILING 

profiling full-length paired V(D)J transcripts using Chromium Single Cell V(D)J Solution

We use Chromium Single Cell V(D)J Solution for profiling full-length paired V(D)J transcripts from hundreds to millions of lymphocytes. This approach enables assembly of full-length V(D)J sequences on a cell-by-cell basis, providing high resolution insights into the adaptive immune system.

Transcriptome approaches are increasingly viable also for organisms lacking a sequenced genome. De novo assembly of RNA-Seq data allows for transcriptome studies for non-model organisms lacking well-defined genomes or for cancer samples, permitting downstream RNA-Seq analyses.

We provide sequencing of RNA-binding protein immunoprecipitation that maps RNA-protein associations in vivo by discovering genome-wide RNA molecules of any type that physically interact with a regulatory protein or protein complex.

 

Multiple single-end and paired-end read length options are available (50bp, 75bp, 125bp, 150bp).

 

BIOINFORMATICS SERVICES

  • Quality control and alignment to a reference
  • Analyses of whole transcriptome with option to unambiguously identify PCR duplicates
  • Differential expression analysis
  • Allele-specific expression analysis
  • Detection of new exons, splice variants and gene fusions
  • Single Nucleotide Variation discovery
  • Strand-specific analysis
  • Unsupervised analysis: Principal Component Analysis (PCA plot) and heatmap
  • Supervised analysis: For each specific group comparison we generate a Volcano plot to display RNAs which are differentially expressed between the groups, list differentially expressed RNAs as well as identify statistically significant signals
  • Non-coding RNA analysis
  • De novo assembly
  • RIP-Seq analysis
  • Single-cell expression profiling (Chromium System, 10xGenomics)
 
 
TAILORED CONSULTANCY

For every project we want to make sure that the outcome will meet your expectations

We also provide full support on study design to ensure correct sequencing and bioinformatics strategies are used to meet your project goals. Our expert will consult with you about your specific requirements, and will also be your technical resource and point of contact for the length of your project. See bioinformatics.

 

Documents & Reports

Samples Spreadsheet v2.xlsx

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RNA and smallRNA Sample preparation guidelines.pdf

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Mammalian APE1 controls miRNA processing and its interacomes is linked to cancer RNA metabolism.pdf

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IGA Depli RNA web.pdf

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Terms and Conditions v3 2017.pdf

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