MARGenomics offers a great variety of services, including all the steps of sample processing and data analysis.

 

If your project needs a different approach from the listed below or a customized solution,

do not hesitate to contact us at margenomics@imim.es.

General support

  • Experimental design of NGS/microarrays/qPCR
  • Customized solutions
  • Manuscript preparation
  • Grant writing support
  • Statistical analysis and bioinformatic tools consulting
  • Best practices
  • Data submission to eg. GEO, EGA, SRA

Extraction Unit

Nucleic Acid Extraction: RNA and DNA extraction from different sample types, including total blood, frozen tissue, FFPE samples, etc. using specific protocols for each kind to obtain the maximum quality.

Nucleic Acid Extraction

  • RNA and DNA extraction from different sample types, including total blood, frozen tissue, FFPE samples, etc:
    • using specific protocols for each kind to obtain the maximum quality

EXTRACTION TEAM

person

Beatriz Bellosillo

Head of Extraction Unit

+34 932483561

bbellosillo@psmar.cat

LAB UNIT

The Laboratory Unit (LU) supports researchers by processing samples to obtain different kinds of omics data. It has more than ten years of expertise of working with all types of samples such as serum, plasma, FFPE, whole blood, swabs etc. LU has been involved in projects from basic research to clinical routine, and accepts queries both from public and private institutions. If the list of offered services does not cover your needs, do not hesitate to contact the facility and a custom solution will be provided.

Next-Generation Sequencing: library preparation for Illumina

  • RNA seq library preparation:
    • Globin/ribosomal depletion
    • PolyA capture
    • Exome capture
  • DNA seq library preparation:
    • Exome capture
    • ATAC-seq
  • smallRNA seq library preparation:
    • smallRNA seq (standard samples)
    • smallRNA seq (low input samples such as serum/plasma)
  • Panels:
    • 16S/ITS panel
    • Custom panel

Microarrays: Thermofisher platform (Affymetrix)

  • Expresion microarrays: for human, mouse and rat. Other species are available.
    • Clariom D/S (specific protocols for standard, degraded or FFPE samples)
    • Gene 2.0/Human Transcriptome Array
    • miRNA arrays
  • Genomic microarrays:
    • Cytoscan HD
    • Cytoscan 750K
    • OncoScan (designed for FFPE samples)

Quantitative PCR (qPCR)

  • Taqman Low Density Arrays: custom design specific for each project.
  • Individual qPCR

Quality sample checking

  • Nanodrop quantification:
    • RNA
    • DNA: ssDNA and dsDNA
  • Qubit quantification:
    • RNA
    • smallRNA
    • dsDNA
  • Bioanalyzer:
    • Nanochip
    • Picochip
    • High sensitivity DNA
    • DNA 1000
  • Agarose gels

LAB TEAM

1_0004_Grupo 5

Marta Bódalo

Head of Laboratory Unit

+34 933160577

mbodalo@imim.es

1_0005_Grupo 6

Maria Gabarrós

Research Technician

+34 933160577

mgabarros@imim.es

1_0000_Grupo 1

Miquel Clarós

Research Technician

+34 933160577

mclaros@imim.es

Bioinformatics Unit

The Bioinformatics Unit (BU) provides computational expertise to process high-throughput omics data (eg. NGS, microarrays) with a special focus on translational research. The facility currently maintains standardized data processing pipelines for basic NGS analyses (eg. QC, alignment, expression analysis, variant calling), but also performs advanced analysis tailored to each service.

 

You can visit our GitHub page at https://github.com/margenomics

Transcriptomics analysis

  • RNA-seq analysis:
    • QC, alignment, transcript/gene quantification, differential transcript/gene expression analysis, alternative splicing analysis, fusion genes, variant calling
  • smallRNA-seq analysis:
    • QC, alignment, miRNA and other small RNA species quantification, differential expression analysis, dmall RNA prediction, miRNA-target analysis
  • Microarray analysis:
    • QC, normalization, differential expression analysis, differential isoform expression analysis, validation of RNA-seq results
  • Single cell RNA-Seq analysis:
    • QC, alignment, transcript/gene quantification, differential expression, identification of cell subtypes and hierarchical markers, trajectory analysis, visualization and clustering
  • Functional analysis of differentially expressed genes or transcripts:
    • Gene set (eg. GO, KEGG) and pathways enrichment analysis (GSEA, ORA, GSVA)
  • Identification of batch effects and data visualization:
    • Heatmaps, dendrograms, Kaplan-Meier, PCAs, Venn diagrams, volcano plots, t-SNE plots, regulatory networks, IGV…
  • Deconvolution of cellular populations:
    • Estimation of the proportion of cellular populations comprised in a bulk sample

Genomics analysis

  • Whole exome/genome sequencing analysis:
    • QC, alignment, variant calling (SNVs, indels, CNVs, structural variants) in somatic and germline samples
  • Visualization:
    • Oncoplots/waterfall, circos plot, lollipop plots, IGV, gene coverage, copy number plots..
  • Variant annotation and interpretation:
    • Identification of pathogenic variants, cancer driver gene mutations, significantly mutated genes…
  • Cancer genomics:
    • Mutational signatures analysis, mutation burden, tumor heterogeneity and purity, clonality of mutations, co-occurrence and mutual exclusivity
  • Neoantigen prediction and MHC binding analysis

Other data analysis

  • Reanalysis of public data:
    • Perform several analyses with public data from different public data repositories (eg. GEO, TCGA, EGA, SRA)
  • Integromics:
    • Integrate multi-omics datasets (eg. genomics, transcriptomics, epigenomics)
  • Analysis of B and T cell repertoires (AIRR):
    • Germline allele assignment, identification of clones, visualization of clonal frequencies
  • Metagenomics:
    • Identification of microbial communities, taxonomic diversity, abundances, phylogenetic analysis from amplicon or shotgun sequencing data
  • Epigenomics:
    • Analysis of global epigenetic changes via several high-throughput technologies (eg Chip-Seq, ATAC-Seq, microarrays)
  • Analysis of qPCR

BIOINFORMATICS TEAM

1_0003_Grupo 4

Júlia Perera Bel

Head of Bioinformatics Unit

+34 933160628

jperera@imim.es

1_0002_Grupo 3

Ariadna Acedo

PhD student

+34 933160628

aacedo@imim.es

MBSU

The consulting service on methodology for biomedical research (MBSU) objective is to offer support on methodology and statistics applied to biomedical research to investigators of Parc de Salut Mar health care centers as well as to investigators from IMIM.

The services offered are:

  • Consulting on study design: Sample size calculation and proposal for statistical
    analysis.
  • Design, management and quality control of data bases developed in any data entry
    environment. Support and monitoring on REDCap use. Final validation of “Move to
    Prod” requests for REDCap projects.
  • Statistical analysis on demand by using appropriate statistical software (R, STATA,
    SPSS).
  • Consulting on scientific publications, presentations and report writing.
  • Training to users on statistical tools and good practices on clinical data management.

MBSU TEAM

Sin-título-1 (3)

Xavier Duran

Head of MBSU

+34 933160614

xduran@imim.es

FEES

Please find here our list of prices

AENOR

MARGenomics was accredited for working under high quality standards with the ISO 9001:2015 quality certificate

TERMS AND CONDITIONS

The provided services are subject of IMIM SCTs Terms and Conditions