Library Preparation

Library preparation has to be specifically tailored to the research question as well as quantity and quality of the input material.

There is no one-size-fits-all recipe!

We have established various library preparation protocols that we can apply depending on the specific requirements. We are happy to discuss the different possibilities.

Before we start library preparation we check the quality of each sample by means of length profiling (AATI Fragment Analyzer, Agilent TapeStation 4200, Agilent BioAnalyzer) and determine the concentration with Pico- or RiboGreen in our lab.

The Genomics Team can prepare sequencing libraries for the following applications

genomic DNA-Seq (incl. PCR-free)
RNA-Seq (stranded, poly(A), rRNA depleted, non-stranded, low input, single-cell)
ChIP-Seq
small RNA-Seq
Agilent SureSelect target capture / Exome sequencing (automated with Agilent Bravo Workstation)
Agilent HaloPlexHS for gene panel sequencing using molecular barcodes
16S sequencing

Users can also submit libraries they prepared themselves. E.g. libraries for the following applications have to be provided by the users:

CLIP-Seq
RAD-Seq
ATAC-Seq
HiC

QC and concentration measurements

The Genomics Team can perform the QC and pool indexed libraries. QC of libraries is performed by AATI Fragment Analyzer, Agilent TapeStation, Agilent Bioanalyzer 2100 and Picogreen measurements.

Sample requirements for library preparation

before submitting the samples

genomic DNA: depending on sample prep protocol 1 ng (0.2 ng/µl) - 3 µg (50 ng/µl)
RNA
- standard gene expression profiling and transcriptome analysis 0.1-1µg total RNA
- low input RNA: 20 pg - 10 ng
- single-cell: please inquire
Agilent SureSelect target capture: 200-3'000 ng depending on protocol
Agilent HaloPlexHS: 50-200 ng
ChIP: 1-10 ng ChIP-enriched, fragmented DNA (We recommend to optimize chromatin shearing to get 150-300 bp fragments. Always tell us the chromatin size; ideally show us an agarose picture or profilie of purified input DNA so we can check the quality.)

Container

When submitting >15 samples/libraries please use Eppendorf TwinTec 96-well plates, skirted. Order the samples in columns: A1-H1, A2-H2, A3-H3....H12=EMPTY. For less samples/libraries you can use 1.5 ml tubes, ideally low binding (e.g. Eppendorf).