Gene expression analysis

Description

The 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 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 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 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 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

Abdelmalek ALIOUA

Ingénieur de recherche / Research engineer
Sandrine KOECHLER

Ingénieure de recherche / Research engineer

Recent publications

All publications

JOHANN TO BERENS P., PETER J., KOECHLER S., BRUGGEMAN M., STAERCK S. and MOLINIER J.

The histone demethylase JMJ27 acts during the UV-induced modulation of H3K9me2 landscape and facilitates photodamage repair

Nature Plants, 0, 2024. | DOI : https://doi.org/10.1038/s41477-024-01814-9
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/kiad278
ARSÈNE-PLOETZE F., ROMPAIS M., ALIOUA A., COGNAT V., ERHARDT M., GRAINDORGE S., KOECHLER S., MUTTERER J., CARAPITO C. and SCHALLER H.

Streptomyces cocklensis DSM 42063 and Actinacidiphila bryophytorum DSM 42138 colonize Arabidopsis thaliana and modulate its proteome

Phytofrontiers, , 2023. | DOI : doi.org/10.1094/PHYTOFR-12-22-0149-R
ALIOUA A. and HEITZLER P.

On the origin of the cultivated roses: DNA authentication of the Bourbon rose founding pedigree.

International Journal of Plant Biology, 14:1117-1130, 2023. | DOI : doi.org/10.3390/ijpb14040082
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.