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Applications

Dear researcher,

here we provide information about Next Generation Sequencing technologies supported by the Cologne Center for Genomics and the Cologne production site of the West German Genome Center.

Who can make use of our platforms?

Every group from the University or University Hospital of Cologne, all groups from both Clusters of Excellence CECAD and CEPLAS will be supported on our standard applications (see list below in bold). If other protocols we provide or substantial changes to our protocols or new implementations are needed, we have to decide on an individual basis if and how we can help, please contact us! All innovative contributions both in lab work and in bioinformatics should be assessed as a scientific collaboration.

All projects that are funded by the NGS-calls of the DFG will be supported in all matters confirmed on the West German Genome Center counseling reports.

All other national and international research groups are welcome to discuss their projects with us to set off a scientific collaboration if sequencing capacity allows. Please note that external prices will be charged. We will not accept requests in commercial or diagnostic settings.

What are the NGS protocols/applications we provide (standards with guaranteed support and data quality and amount in bold, DNA= blue, RNA=red, EPI=green)?

 

ApplicationProtocolComments/special features
PCR-free genome TruSeq, modified  
Low-input genome Nextera flex e.g. single worm
AmpliconDeepSeq TruSeq, Qiagen e.g. Metagenomics/HLA
Small genome/long-range PCR products NexteraXT  
Exome, gene panel SureSelect: XT, QXT, HS, NimbleGen different species, custom and standard, UMI for HS protocol, FFPE experience with modified protocol
Small gene panel TruSeq Amplicon  
ATAC Nextera  
HiC inhouse (Illumina MatePair or SureSelect HS) HiC, easyHiC, HiChiP
RADseq published protocol  
Linked-read genomes 10x Genomics  
mRNAseq TruSeq stranded  
Total RNAseq TruSeq Ribo-zero (gold) different depletion kits, dual transcriptomics
3´RNAseq Lexogen  
Low-input RNAseq NuGEN (Nextera)  
3´scRNAseq 10x Genomics  
scRNAseq on Nuclei 10x Genomics  
Full-length scRNAseq WaferGen Takara  
ribo-seq    
circRNASeq   native cycles
circSeq published protocol artificial cycles for RNA editing analysis
transient RNASeq 4US, SLAMseq, TTseq  
ChiP-seq TruSeq, modified  
TADA (targeted DAMID) published protocol  
miRNA TruSeq or Lexogen  
MethylSeq NEB beta-Test on cfDNA
WGBS Illumina  
Targeted BS e.g. Ilumina or Agilent  
RIP-seq, PARclip, eCLIP published protocols  

 

Our current platforms include Illumina sequencers (NovaSeq6000, HiSeq4000 and MiSeq) and Oxford Nanopore long-read single molecule technology (GridION).

How to submit samples?

Please request the newest version of the suitable submission form from us. This should be filled in advance before sending samples. Cost information will be provided once the experimental design has been completed.

High quality data and requested data amount is guaranteed for standard applications where samples fulfill the following requirements:

Sample requirements for RNAseq and miRNAseq experiments:2µg total RNA, concentration range 50-200ng/µl, at least 10µl volume. DNA free, no degradation (RIN > 7), OD260/280 = 1,8-2,1 and OD260/230 >1,5. Please use clearly labeled 1,5ml Eppendorf tubes.

Sample requirements for Genome Sequencing, PCR-free: 3μg high molecular DNA, concentration 50-100ng/μl (at least 10μl volume), no degradation, attach a gel picture (50ng DNA on a 0,7% agarose gel), clearly labeled 1,5ml Eppendorf tubes.

Sample requirements for Amplicon sequencing: 1μg colum purified PCR-Product (at least 10μl volume, concentration 10-100ng/μl, attach a gel picture (50ng DNA on a 0,7% agarose gel), clearly labeled 1,5ml Eppendorf tubes. Make sure that the read length chosen fits to the size of your amplicons.

Sample requirements for ChIPseq: At lease 10ng ds ChIP DNA (more is better) in a max. volume of 50μl. dsDNA fragments should be in a range of 300-500bp, clearly labeled 1,5ml Eppendorf tubes. Please note that we will not do any QC steps with this kind of material to make full use of what you give us.

Sample requirements for WES (whole exome sequencing) or GPS (gene panel sequencing): 2µg genomic DNA, concentration range 50-100ng/µl, at least 20µl volume No degradation. Please attach a gel picture (0,7% agarose). Please use clearly labeled 1,5ml Eppendorf tubes.

Please contact us before you send the samples if you can't meet these criteria. We will probably have another protocol to support your project.

Samples can be handed over Mo-Fr between 9 am and 4 pm to any member of the NGS team if a printed sample sheet is enclosed. Average TAT for standard experiments is 4 weeks. Sample requirements for Single Cell RNA seq (for partners who co-financed the 10x Genomics Chromium system only):

700-1200 cells/µL concentration, viability (> 75%), Medium: 1XPBS containing 0,04% BSA Diameter <40µm, Single cell suspension, free of debris and cell aggregates. Scheduling of these experiments is critical - please contact us at least 4 weeks ahead of submitting samples for scRNAseq.

Contact

Most researches, especially if they do one of our application for the first time, will need some introduction and project-specific discussion. Please don´t hesitate to contact us!

Dr. Janine Altmüller
NGS Core Facility Leader
Cologne Center for Genomics (CCG)
and West German Genome Center (WGGC)
Universität zu Köln
Weyertal 115b
D-50931 Köln
Tel: +49 221 478 96819
E-mail: