Deep Sequencing Facility

Contact

Deepseqlab@bioquant.uni-heidelberg.de

Office :    +49 (0) 6221 54 51359

Lab :        +49 (0) 6221 54 51369

Room 542 / 606 BioQuant Building

Sample Registration site : https://hmls.corefacilities.org

User Aggreement : Nutzerordnung Deep Seq Lab Final

 

 

+++ Important Information Regarding Deep Sequencing Core Facility during Corona Pandemic +++

 

Due to the current Corona virus pandemic, the University of Heidelberg has implemented a partial closure. This has led to the following consequences for the Deep Sequencing Core Facility:

1) The Facility is currently closed on Tuesday, Fridays and every second Wednesday so long as school closures are implemented.

2) Meetings will no longer take place face-to-face, and as such I would recommend e-mail or organising telephone calls to discuss any projects.

3) The BioQuant building is now keycard access only, so please contact the core facility in advance if you wish to bring samples or use the Covaris. Personally given the current situation I would advise against using the Covaris until the restrictions are lifted.

4) To minimise contact between people due to the small area of my lab only two people at any one time will be allowed into the room to use the instruments.

5 )Please have understanding due to the restrictions and also difficulties in deliveries, processing of the samples will take longer. We are finding ourselves in an unusual situation, with new restrictions being brought in almost daily, I again appeal for understanding here.

Thanks for your understanding and support.

The Facility wishes its Users that you all stay healthy, keep safe and we hope that this all is over soon.

 

Deep Sequencing Core Facility

 

Website is under Construction

 

 

 

Introduction

The CellNetworks Deep Sequencing Core Facility was opened in September 2010 to provide access to Next Generation Sequencing technology (NGS), for the Heidelberg University research community. The Core Facility is supported by the Excellence Cluster CellNetworks, the Centre for Organismal Studies (COS Heidelberg), Heidelberg Molecular Life Sciences (HMLS) Research Council and the Excellence Strategy  Field of Focus 1.

Core Facility Concept and Services Provided

The facility was founded with the intent to not only to provide library preparation and sequencing for its users on campus, but also to offer professional advice on how to implement NGS into its users research. This advice has been widely taken up and has in some cases led to the development of new protocols or the refinement of current “standard” protocols. In addition it is widely recommended that users speak with us before initiating a project, in order to clear up any mis-conceptions about NGS, which will inevitably save the researcher's money and time.

With regards to services, the Core Facility offers a mixture of services for its users. The main day to day activities revolve around the standard library preparation methods for Illumina sequencing. However, due to the high diversity in sample genome origin on campus, and the fact that reagents are tailored to samples originating from humans and mice, the library preparations are often tailored to the individual group from which the samples originate.

                “Standard” library preparations on offer:

  • RNA-Seq (as of June 2014 all libraries are strand specific)

  • Small RNAseq

  • Chip-Seq

  • gDNA-Seq (de novo, resequencing)

  • Target Enrichment

  • Single Cell Sequencing

  • Single Cell on 10x Chromium Platform

 

 

Instrumentation:

The Core Facility has in the previous years maintained a successful collaboration with the Genomics Core Facility of EMBL. Due to this we have access to the following sequencing instruments:

1) NextSeq 550 - A desktop based sequencer with quick turn around time and high sequencing adaptability

2) HiSeq 4000 - The large scale/production scale sequencer

3) MiSeq - A desktop sequencer with low output, ideal for testing of new protocols or amplicon libraries.

 

In addition we have the following instruments to help with the library preparation:

1) Covaris S2 sonicator

2) Bioanalyzer - a capillary electrophoresis instrument which aids the analyze RNA quality and view the library products prior to sequencing.

3) 10x Chromium System - single cell capture system for transcription profiling and ATACseq. This is currently a staff use only instrument.

 

Feel free to contact us for further questions, have a look at our user agreement.

 

 

Contact

Deepseqlab@bioquant.uni-heidelberg.de

Office :    +49 (0) 6221 54 51359

Lab :        +49 (0) 6221 54 51369

Room 542 / 606 BioQuant Building

Sample Registration site : https://hmls.corefacilities.org

User Aggreement : Nutzerordnung Deep Seq Lab Final


 

 

 

 

Selected Publications and Acknowledgements:

Mugo E, Clayton C. Expression of the RNA-binding protein RBP10 promotes the bloodstream-form differentiation state in Trypanosoma brucei. Read L, ed. PLoS Pathogens. 2017;13(8):e1006560. doi:10.1371/journal.ppat.1006560.

Klein C, Terrao M, Clayton C. The role of the zinc finger protein ZC3H32 in bloodstream-form Trypanosoma brucei. Li Z, ed. PLoS ONE. 2017;12(5):e0177901. doi:10.1371/journal.pone.0177901.

Mulindwa J, Mercé C, Matovu E, Enyaru J, Clayton C. Transcriptomes of newly-isolated Trypanosoma brucei rhodesiense reveal hundreds of mRNAs that are co-regulated with stumpy-form markers. BMC Genomics. 2015;16:1118. doi:10.1186/s12864-015-2338-y.

Fadda A, Ryten M, Droll D, et al. Transcriptome-wide analysis of trypanosome mRNA decay reveals complex degradation kinetics and suggests a role for co-transcriptional degradation in determining mRNA levels. Molecular Microbiology. 2014;94(2):307-326. doi:10.1111/mmi.12764.

A Genome-Wide Tethering Screen Reveals Novel Potential Post-Transcriptional Regulators in Trypanosoma brucei
Erben ED, Fadda A, Lueong S, Hoheisel JD, Clayton C (2014) A Genome-Wide Tethering Screen Reveals Novel Potential Post-Transcriptional Regulators in Trypanosoma brucei. PLOS Pathogens 10(6): e1004178. https://doi.org/10.1371/journal.ppat.1004178

Mulindwa J, Fadda A, Merce C, Matovu E, Enyaru J, Clayton C. Methods to Determine the Transcriptomes of Trypanosomes in Mixtures with Mammalian Cells: The Effects of Parasite Purification and Selective cDNA Amplification. Raper J, ed. PLoS Neglected Tropical Diseases. 2014;8(4):e2806. doi:10.1371/journal.pntd.0002806.

Singh A, Minia I, Droll D, Fadda A, Clayton C, Erben E. Trypanosome MKT1 and the RNA-binding protein ZC3H11: interactions and potential roles in post-transcriptional regulatory networks. Nucleic Acids Research. 2014;42(7):4652-4668. doi:10.1093/nar/gkt1416.

Fadda A, Färber V, Droll D, Clayton C. The roles of 3′-exoribonucleases and the exosome in trypanosome mRNA degradation. RNA. 2013;19(7):937-947. doi:10.1261/rna.038430.113.

Droll D, Minia I, Fadda A, et al. Post-Transcriptional Regulation of the Trypanosome Heat Shock Response by a Zinc Finger Protein. Ullu E, ed. PLoS Pathogens. 2013;9(4):e1003286. doi:10.1371/journal.ppat.1003286.

Nat Commun. 2015 Apr 8;6:6753. doi: 10.1038/ncomms7753. Transcriptional refractoriness is dependent on core promoter architecture. Cesbron F1, Oehler M1, Ha N1, Sancar G1, Brunner M1.

Sancar C, Ha N, Yilmaz R, et al. Combinatorial Control of Light Induced Chromatin Remodeling and Gene Activation in Neurospora . Kramer A, ed. PLoS Genetics. 2015;11(3):e1005105. doi:10.1371/journal.pgen.1005105.

Sancar C, Sancar G, Ha N, Cesbron F, Brunner M. Dawn- and dusk-phased circadian transcription rhythms coordinate anabolic and catabolic functions in Neurospora. BMC Biology. 2015;13:17. doi:10.1186/s12915-015-0126-4.

Zhou Y, Zhu J, Schermann G, et al. The fission yeast MTREC complex targets CUTs and unspliced pre-mRNAs to the nuclear exosome. Nature Communications. 2015;6:7050. doi:10.1038/ncomms8050.

Dev Cell. 2017 Sep 11;42(5):462-478.e7. doi: 10.1016/j.devcel.2017.08.002. Epub 2017 Aug 31. YAP/TAZ Orchestrate VEGF Signaling during Developmental Angiogenesis.Wang X1, Freire Valls A2, Schermann G1, Shen Y3, Moya IM4, Castro L1, Urban S1, Solecki GM5,

Winkler F5, Riedemann L6, Jain RK6, Mazzone M7, Schmidt T3, Fischer T8, Halder G4, Ruiz de Almodóvar C9.
Gumiero A, Conz C, Gesé GV, et al. Interaction of the cotranslational Hsp70 Ssb with ribosomal proteins and rRNA depends on its lid domain. Nature Communications. 2016;7:13563. doi:10.1038/ncomms13563.

Patel PH, Dutta D, Edgar BA. Niche Appropriation by Drosophila Intestinal Stem Cell Tumors. Nature cell biology. 2015;17(9):1182-1192. doi:10.1038/ncb3214.

Curr Protoc Stem Cell Biol. 2015 Aug 3;34:2F.2.1-14. doi: 10.1002/9780470151808.sc02f02s34.Regional Cell Specific RNA Expression Profiling of FACS Isolated Drosophila Intestinal Cell Populations.Dutta D1, Buchon N2, Xiang J1, Edgar BA1.

Cell Rep. 2015 Jul 14;12(2):346-58. doi: 10.1016/j.celrep.2015.06.009. Epub 2015 Jul 2.Regional Cell-Specific Transcriptome Mapping Reveals Regulatory Complexity in the Adult Drosophila Midgut.Dutta D1, Dobson AJ2, Houtz PL2, Gläßer C1, Revah J2, Korzelius J1, Patel PH1, Edgar BA3, Buchon N4.

EMBO J. 2014 Dec 17;33(24):2967-82. doi: 10.15252/embj.201489072. Epub 2014 Oct 8. Escargot maintains stemness and suppresses differentiation in Drosophila intestinal stem cells. Korzelius J1, Naumann SK1, Loza-Coll MA2, Chan JS1, Dutta D1, Oberheim J1, Gläßer C1, Southall TD3, Brand AH3, Jones DL2, Edgar BA4.

Curr Protoc Stem Cell Biol. 2013 Nov 13;27:Unit 2F.2.. doi: 10.1002/9780470151808.sc02f02s27. RNA expression profiling from FACS-isolated cells of the Drosophila intestine. Dutta D1, Xiang J, Edgar BA.

Eur Respir J. 2017 Oct 5;50(4). pii: 1701086. doi: 10.1183/13993003.01086-2017. Print 2017 Oct. Chronic but not intermittent infection with Pseudomonas aeruginosa is associated with global changes of the lung microbiome in cystic fibrosis. Boutin S1,2, Graeber SY2,3,4, Stahl M2,3,4, Dittrich AS2,4,5, Mall MA2,3,4,6, Dalpke AH7,2,6.

Boutin S, Hagenfeld D, Zimmermann H, et al. Clustering of Subgingival Microbiota Reveals Microbial Disease Ecotypes Associated with Clinical Stages of Periodontitis in a Cross-Sectional Study. Frontiers in Microbiology. 2017;8:340. doi:10.3389/fmicb.2017.00340.

Boutin S, Graeber SY, Weitnauer M, et al. Comparison of Microbiomes from Different Niches of Upper and Lower Airways in Children and Adolescents with Cystic Fibrosis. Coenye T, ed. PLoS ONE. 2015;10(1):e0116029. doi:10.1371/journal.pone.0116029.

Cell. 2013 May 9;153(4):869-81. doi: 10.1016/j.cell.2013.04.016. Roquin promotes constitutive mRNA decay via a conserved class of stem-loop recognition motifs. Leppek K1, Schott J, Reitter S, Poetz F, Hammond MC, Stoecklin G.

Mol Cell. 2016 Sep 15;63(6):927-38. doi: 10.1016/j.molcel.2016.08.030. Acetylation-Dependent Control of Global Poly(A) RNA Degradation by CBP/p300 and HDAC1/2. Sharma S1, Poetz F1, Bruer M1, Ly-Hartig TB1, Schott J1, Séraphin B2, Stoecklin G3.

Schott J, Reitter S, Philipp J, Haneke K, Schäfer H, Stoecklin G. Translational Regulation of Specific mRNAs Controls Feedback Inhibition and Survival during Macrophage Activation. Wells CA, ed. PLoS Genetics. 2014;10(6):e1004368. doi:10.1371/journal.pgen.1004368.

Gutierrez-Triana JA, Mateo JL, Ibberson D, Ryu S, Wittbrodt J. iDamIDseq and iDEAR: an improved method and computational pipeline to profile chromatin-binding proteins. Development (Cambridge, England). 2016;143(22):4272-4278. doi:10.1242/dev.139261.

Hohmann N, Wolf EM, Lysak MA, Koch MA. A Time-Calibrated Road Map of Brassicaceae Species Radiation and Evolutionary History. The Plant Cell. 2015;27(10):2770-2784. doi:10.1105/tpc.15.00482.

Petersen HO, Höger SK, Looso M, et al. A Comprehensive Transcriptomic and Proteomic Analysis of Hydra Head Regeneration. Molecular Biology and Evolution. 2015;32(8):1928-1947. doi:10.1093/molbev/msv079.

 

 

Steering Commitee:

  • Dr. May-Britt Becker (CellNetworks)
  • Prof. Dr. Michael Brunner (BZH)
  • Prof. Dr. Thomas Holstein (COS)
  • Prof. Dr. Jochen Wittbrodt (COS)

 

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Letzte Änderung: 26.06.2020
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