Gene expression analysis

Leader: Abdelmalek ALIOUA

Description

The goal of the Gene Expression Analysis Platform (AEG) is to provide to public and private research teams some tools and competences for the realization of their research projects related to genomics, transcriptomics and epigenetics .
This technology platform is shared between 3 research units from Strasbourg, IBMC, GMGM and IBMP.

The platform has instruments for the realization of sequencing projects (Oxford Nanopore, NGS-Illumina and Sanger), genotyping (HRM) and gene expression analysis (qPCR)

Expertises

Long read sequencing | Oxford Nanopore Technologies

Manager : Abdelmalek ALIOUA

Preparation and validation of DNA and RNA libraries. Sequencing on the Oxford Nanopore MinIon device. Quick service and support for projects.

Applications:

  • Genome sequencing
  • Sequencing of complete transcripts
  • Genomic & epigenetic editing

Output :

  • 2048 pores / 512 channels
  • Up to 20 Gb in 48 hours
  • Multiplexing

Next Generation Sequencing | MiSeq illumina

Manager : Sandrine KOECHLER

Libraries construction and QC, DNA sequencing on the MiSeq instrument

Applications:

  •   16S rRNA gene sequencing
  •   amplicons sequencing
  •   whole genome sequencing
  •   small RNA sequencing

Output:

  •    up to 50 millions paired end reads
  •    up to 15Gb (maximum length 2X300 in 56 hours)
  •    multiplexing possibilities
  •    short delivery times

Sanger DNA sequencing and capillaries electrophoresis genotyping | ABI3130 XL

Manager : Abdelmalek ALIOUA

Applications:

  • sequencing of various templates (PCR, plasmids)
  • direct sequencing on bacterial culture
  • SSR genotyping

 

Output:

  • 384 sequences in 24 hours
  • up to 1000 bases resolution

qPCR analysis of gene expression | Roche LC480 – 384 puits

Manager : Abdelmalek ALIOUA

For high-throughput quantitative real-time PCR gene expression analysis projects, the platform offers a variety of services :

  • user training
  • drawing and validation of primers for the Sybrgreen method
  • relative and absolute quantification
  • validation of RNA-seq results
  • rapid service and project management

 

Output:

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

 

High throughput HRM genotyping | Roche LC480 – 384 puits

Manager : Abdelmalek ALIOUA

HRM is a and cost-effective method for high throughtput genotyping.

Applications:

  • SNP genotyping
  • Screening of Crispr/Cas9 mutants
  • Indels mutations detection
  • Detection and quantification of DNA methylation
  • Pathogen detection

Output:

  • up to 192 samples per run (2 h)
  • short delivery times

Digital PCR | Stilla Naica

Manager : Sandrine KOECHLER

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 DNA methylations
  • Detection and quantification of rare or low abundance RNAs
  • Detection and quantification of alternative transcripts
  • Analysis of miRNAs
  • Copy number variation (CNV)
  • Mutation detection (i.e SNP)
  • Detection of pathogens (viral loads, microbiome analysis)
  • Quantification of NGS libraries

Output:

  • 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

All publications

  • 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 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 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 logo

  • SCHEER H., DE ALMEIDA C., SIKORSKA N., KOECHLER S., GAGLIARDI D. and ZUBER H.

    High-Resolution Mapping of 3’ Extremities of RNA Exosome Substrates by 3’ RACE-Seq

    In: LaCava J, Vaňáčová Š (eds) The Eukaryotic RNA Exosome. Methods in Molecular Biology, vol 2062. Humana New York, NY., 2020. | DOI logo

  • FREEL K.C., FOUTEAU S., ROCHE D., FARASIN J., HUBER A., KOECHLER S., PERES M., CHIBOUB O., VARET H., PROUX C., DESCHAMPS J., BRIANDET R., CRUVEILLER S., LIÈVREMONT D., COPPÉE J.Y., BARBE V. and ARSÈNE-PLOETZE F.

    Effect of arsenite and growth in biofilm conditions on the evolution of Thiomonas sp. CB2

    Microbial Genomics, 6(10):mgen00044, 2020. | DOI logo

IBMP Labels

CNRS
Université de Strasbourg
ANR
European Research Council
Investir l’Avenir
H2020
HFSP
Conectus
interreg
cost-actions
Vitifutur
MitoCross
NetRNA