Gene expression analysis

Leader: Abdelmalek ALIOUA

Description

The AEG platform is specialized in nucleic acids sequencing and genes expression analysis. Strategically, it constitutes a center of expertise in “long reads” sequencing with Oxford Nanopore technology.
The objectives of the platform are to provide public and private research teams with tools and skills to carry out their projects in genomics, transcriptomics and epigenetics. It has new generation instruments for NGS sequencing (Oxford Nanopore and Illumina), high-throughput Crispr-Cas9 genotyping (HRM) and genes expression analysis (qPCR and ddPCR).
The AEG platform is defined according to a charter. It offers services according to a price list, and research collaborations for the implementation of projects with the development of specific methods.

Networks
The AEG platform is a member of Cortecs, a network of scientific research and service platforms of the University of Strasbourg, in partnership with CNRS and INSEM.
The AEG platform labeled IBiSA , a scientific interest group (GIS) which conducts a selective national policy of labeling and support for biology, health and agronomy platforms and biological resource centers (CRB).

Equipments

  • Oxford Nanopore Sequencing: PromethION P2 and 2 MinION with Flongle Adapter
  • Illumina NGS sequencing: MiSeq
  • Digital PCR: Stilla Naica System
  • Genes expression analysis by qPCR and HRM genotyping: Roche LC480-II
  • Quality control of NGS sequencing samples and libraries: Bioanalyzer 2100 (Agilent); Qubit (ThermoFisher Scientific)

How to submit a project to the platform?
To submit a project to the AEG platform, contact us by email at ibmp-aeg@unistra.fr
We will respond to you within 7 days to define the best strategy to adopt and the technological approach to consider. An cost estimation will then be drawn up. The deadline for carrying out the experiments will be communicated to you after validation of the samples. In some cases, an exchange with a bioinformatician will be proposed to you before the launch of the project.

Expertises

NGS Long reads sequencing | Oxford Nanopore

Custom preparation, validation and sequencing of DNA and RNA libraries.

Applications

  • Genome sequencing
  • Amplicon sequencing
  • Targeted sequencing: Adaptive Sampling sequencing
  • Genomic & epigenetic editing: Detection of structural variations
  • Transcriptome sequencing: RNA-seq, cDNA-Seq / splicing variants detection
  • MicroRNome sequencing: small RNA-seq, detection of structural variations

Throughput

  • 800 to 2675 pores
  • Up to 100 Gb in 72 hours
  • Multiplexing

NGS short reads sequencing | Illumina

Custom preparation, validation and sequencing of DNA and RNA libraries.

Applications

  • Genome and amplicon sequencing
  • Genomic & epigenetic editing: Chip-seq
  • Transcriptome sequencing: RNA-seq
  • MicroRNome sequencing: small RNA-seq, Mime-seq
  • Ribosome profiling: Ribo-seq
  • Microbiome sequencing: 16S-rRNA-seq

Throughput

  • Up to 50 million paired-end reads
  • Maximum sequencing length: 1 x 600 cycles or 2 x 300 cycles in 56 hours)
  • Up to 15 Gb of data
  • Custom multiplexing

Full length plasmids sequencing

We offer service for full length sequencing and de novo assembly of your plasmids (insert and/or vector).

Applications

  • Validation of the backbone of your plasmids
  • Validation of your cloning, full length sequencing of inserts

Throughput

  • Up to 192 plasmids in parallel
  • Automated de novo assembly

Genes expression analysis by qPCR | Roche LC480

High-throughput genes expression analysis by real-time quantitative PCR. The platform offers various services:
Applications

  • Design and validation of primers and probes
  • Relative and absolute quantifications
  • Validation of RNA-seq results
  • Quantification of NGS libraries

Throughput

  • 384-well PCR block for high-throughput analysis
  • Up to 8 runs in 24 hours

High throughput HRM genotyping | Roche LC480

The HRM is a cost-effective method for high-throughput genotyping.
Applications

  • SNP genotyping (classes 1 to 4)
  • Crispr/Cas9 Mutant Screening
  • Detection of indel mutations
  • Detection and quantification of DNA methylations
  • Identification of pathogens

Throughput

Up to 192 samples in 2 hours

Digital PCR | Stilla Naica

Digital PCR is the third generation of PCR after endpoint PCR and real-time PCR. This technology allows a very precise numerical quantification of the nucleic acids contained in the biological samples.
Applications

  • Absolute quantification & gene expressions (<2 x differences)
  • Detection and quantification of rare or low abundance RNAs
  • Detection and quantification of alternative transcripts
  • miRNA analyzes
  • Copy Number Variation (CNV)
  • Pathogen detection (viral loads, microbiome analysis)

Throughput

  • Up to 48 chambers per run
  • Analysis of 48 samples in multiplex (3) / detection of 144 targets per run.
  • 20000 droplets/chamber (0.22 nl drop volume)LOD 0.2 copies/µl
  • Dynamic range = 5 log

Members

Recent publications

  • JOLY A.C., GARCIA S., HILY J.M., KOECHLER S., DEMANGEAT G., GARCIA D., VIGNE E., LEMAIRE O., ZUBER H. and GAGLIARDI D.

    An extensive survey of phytoviral RNA 3' uridylation identifies extreme variations and virus-specific patterns

    Plant Physiology, kiad278, 2023. | DOI : 10.1093/plphys/kiad278DOI logo

  • GRAINDORGE S., VILLETTE C., KOECHLER S., GROH C., COMTET-MARRE S., MERCIER P., MAGERAND R., PEYRET P., HEINTZ D., SCHALLER H. and ARSÈNE-PLOETZE F.

    The Arabidopsis thaliana–Streptomyces Interaction Is Controlled by the Metabolic Status of the Holobiont

    International Journal of Molecular Sciences, 23:12952, 2022.

  • SCHEER H., DE ALMEIDA C., FERRIER E., SIMONNOT Q., POIRIER L., PFLIEGER D., SEMENT F., KOECHLER S., PIERMARIA C., KRAWCZYK P., MROCZEK S., CHICHER J., KUHN L., DZIEMBOWSKI A., HAMMANN P., ZUBER H. and GAGLIARDI D.

    The TUTase URT1 connects decapping activators and prevents the accumulation of excessively deadenylated mRNAs to avoid siRNA biogenesis

    Nature Communications, 12:1298, 2021. | DOI : 10.1038/s41467-021-21382-2DOI logo

  • FERTET A., GRAINDORGE S., KOECHLER S., DE BOER G.J., GUILLOTEAU-FONTENY E. and GUALBERTO J.M.

    Sequence of the mitochondrial genome of Lactuca virosa suggests an unexpected role in Lactuca sativa’s evolution

    Frontiers in Plant Science, 12:697136, 2021. | DOI : doi: 10.3389/fpls.2021.697136DOI logo

  • MÉTEIGNIER L.V., GHANDOUR R., MEIERHOFF K., ZIMMERMANN A., CHICHER J., BAUMBERGER N., ALIOUA A., MEURER J., ZOSCHKE R. and HAMMANI K.

    The Arabidopsis mTERF-repeat MDA1 protein plays a dual function in transcription and stabilization of specific chloroplast transcripts within the psbE and ndhH operons

    New Phytologist, 227(5):1376–1391, 2020. | DOI : 10.1111/nph.16625DOI logo