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Analysis platforms

Ausstattung | Equipment

FastPrep 24 (MP Bio); FastPrep 24 is a high-speed homogenisor for biological samples; it can be used for various sample amounts and for up to 24 parallel extractions.

Available extraction kits can be found here:

DNA/RNA Cleanup Einklappen

KingFisher (Thermo); KingFisher devices use magnet-bead technologies for automated cleanup of nucleic acids and proteins. We use kits from several providers, and new kits can be adopted to the KingFisher device.

DNA/RNA Quantification Einklappen

Qubit 3 (Invitrogen); For precise measurement of DNA, RNA, and proteins.

Fragment Analysis and Quality Control Einklappen

Fragment Analyzer (Agilent); This capillary electrophoresis system allows the analysis of up to 288 samples (3x 96 plates) of nucleic acids per run.

Fragment Analyzer is used for QC of NGS libraries, for RNA integrity check, and for fragment analysis of PCR products (e.g. Microsatellites, ISSR).

Analysis kits (more kits upon request):

quantitative NGS kit: DNF-477 (50 - 1500 bp)
qualitative DNA kit: DNF-910 (35 - 1500 bp)
qualitative DNA kit: DNF-915 (35 - 5000 bp)
quantitative and qualitative RNA kit: DNF-470 (15 - 200 nt)
quantitative and qualitative RNA kit: DNF-471 (200 - 6000 nt)
quantitative and qualitative RNA kit: DNF-472 (200 - 6000 nt, high sensitive)

DNA size selection / purification Einklappen

Pippin Prep: DNA size selection system from 100 to 1500 bp. Purification of NGS libraries.

Gel cassette types and target ranges:

1.5% Agarose: 250 - 1500 bp
2% Agarose: 200 - 600 bp
3% Agarose: 120 -250 bp

Next-Generation Sequencing (NGS)Einklappen

iSeq-100 (Illumina); Benchtop NGS device for high-throughput sequencing of small genomes (e.g. bacteria, viruses), microbial genomes (Amplicon Sequencing), and transcriptomes (targeted gene expression profiling, MACE-RNA-seq).

The read length is up to 150 bp in single-end or paired-end mode. It delivers up to 1.8 GB raw data output.

Pipettierroboter Einklappen

Mantis (Formulatrix): Contact-free pipettung robot for volumina from 0.1 µl up to the µl range. It is particularily suited for dispensing of expensive or limited reaction mixtures into 96 or 384 well microtiterplates.

CellSorter Einklappen

CellSorter: This device will be used for identification, isolation, and sorting of single cells. It consists of an inverted microscope and a micromanipulator-controlled capillary. Single cell manipulation is controlled by a dedicated software.

Identification of single cells is possible by ligh microscopy or by fluorescent markers of the cells.

Sequence Analysis / Next-Generation Sequencing Einklappen: © Geneious

Geneious Client & Server: Sequence analysis package for classical molecular biology applications and NGS applications. A powerful Geneious Server is used when demands on memory and CPU is high.
Functional Analysis / Next-Generation Sequencing Einklappen: © OmicsBox/biobam

Omicsbox Pro: Sequence analysis platform for genomics, transcriptomics, functional annotation, and microbiome analyses.
Mikrobiome Analysis / Next-Generation Sequencing Einklappen: © QIIME2.org

Qiime2: Qiime2 (Quantitative Insights Into Microbial Ecology) is a collection of tools for the qualitative and quantitative analysis of Amplicon-Seq data (e.g. 16S, 18S, ITS markers). These workflows cover NGS quality control, taxonomic assignments, phylogentic tree reconstruction, alpha and beta diversity analyses, rarefaction analyses, and other dedicated procedures.
Multivariate Statististical Analysis Einklappen: © Primer-e

Primer-e: Bioinformatics tool for multivariate analyses of biological and ecological data.

Verantwortlich für die Redaktion: PD Dr. Alfons Weig

Fakultät für Biologie, Chemie und Geowissenschaften

Keylab Genomanalytik & Bioinformatik – PD Dr. Alfons Weig

Analysis platforms

Ausstattung | Equipment