MARGenomics offers a great variety of services, including all the steps of sample processing and data analysis. All the submitted requests are managed from a single reception, which also supports the preparation of ethical/legal documents, transfer agreements for the samples and/or data, and preparation of budgets and billing.
SERVICES
EXTRACTION UNIT
Nucleic acid extraction
LAB UNIT
Genomic laboratory
BIOINFORMATICS UNIT
Bioinformatics analysis
General support
- Design of NGS/microarrays/qPCR experiments
- 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
Marta Bódalo
Head of Laboratory Unit+34 933160577
mbodalo@imim.es
Maria Gabarrós
Research Technician+34 933160577
mgabarros@imim.es
Miquel Clarós
Research Technician+34 933160577
mclaros@imim.es
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.
- Genomic microarrays:
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
Marta Bódalo
Head of Laboratory Unit+34 933160577
mbodalo@imim.es
Maria Gabarrós
Research Technician+34 933160577
mgabarros@imim.es
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 BU supports researchers with the experimental design (together with the other MARGenomics units), bioinformatics analysis, visualization and interpretation of the results. The facility currently maintains standardized data processing pipelines for basic NGS analyses (eg. QC, alignment, expression analysis, variant calling, functional analysis), 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
Júlia Perera Bel
Head of Bioinformatics Unit+34 933160628
jperera@imim.es
Ariadna Acedo
PhD student+34 933160628
aacedo@imim.es
FEES
MARGenomics is a core facility from IMIM (Hospital del Mar Medical Research Institute) with more than ten years of experience. An integrated service is offered to public and private organizations, providing tailored solutions to a wide range of projects with a focus on translational research
AENOR
MARGenomics is a core facility from IMIM (Hospital del Mar Medical Research Institute) with more than ten years of experience. An integrated service is offered to public and private organizations, providing tailored solutions to a wide range of projects with a focus on translational research
TERMS AND CONDITIONS
MARGenomics is a core facility from IMIM (Hospital del Mar Medical Research Institute) with more than ten years of experience. An integrated service is offered to public and private organizations, providing tailored solutions to a wide range of projects with a focus on translational research