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.

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

Members

Abdelmalek ALIOUA

Ingénieur de recherche / Research engineer
Sandrine KOECHLER

Ingénieur d'études / Engineer

Recent publications

All publications

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, :, 2020. | DOI : doi.org/10.1111/nph.16625
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

, , 2020. | DOI : 10.1007/978-1-4939-9822-7_8
LE RET M., BELCHER S., GRAINDORGE S., WALLET C., KOECHLER S., ERHARDT M., WILLIAMS-CARRIER R., BARKAN A. and GUALBERTO J.M.

An organellar thymidine kinase is required for the efficient replication of the maize plastidial genome.

Plant Physiology, 178:1643-1656, 2018. | DOI : 10.1104/pp.18.00976
BORTOLAMIOL-BÉCET D., MONSION B., CHAPUIS S., HLEIBIEH K., SCHEIDECKER D., ALIOUA A., BOGAERT F., REVERS F., BRAULT V. and ZIEGLER-GRAFF V.

Phloem-triggered virus-induced gene silencing using a recombinant polerovirus

Frontiers in Microbiology, 9:2449, 2018. | DOI : 10.3389/fmicb.2018.02449
CHEN K., DE BORNE F., SIERRO N., IVANOV N., ALIOUA A., KOECHLER S. and OTTEN L.

Organization of the TC and TE cellular T-DNA regions in Nicotiana otophora and functional analysis of three diverged TE-6b genes

Plant Journal, 94:274-287, 2018. | DOI : 10.1111/tpj.13853

IBMP Labels

HFSP

Conectus

interreg

cost-actions

MitoCross

NetRNA