NIG

NGS Integrative Genomics Core Unit

Dr. Gabriela Salinas
NIG Head
gsalina@gwdg.de

Dr. Orr Shomroni
Bioinformatics Scientist
orr.shomroni@med.uni-goettingen.de

Cong Cao
Bioinformatics Scientist
cong.cao@med.uni-goettingen.de

Susanne Luthin
Technician
sluthin@gwdg.de

Fabian Ludewig
Technician
fabian.ludewig@med.uni-goettingen.de

NIG, NGS Integrative Genomics Core Unit, is a central research service facility at the University Medical Center Göttingen (UMG) and functionally affiliated with the Institute of Human Genetics. We provide resources and services in genomics, transcriptomics and epigenomics to support biomedical research projects by applying next-generation sequencing technologies and microarray methods for genome analysis. Our users have access to extensive expertise and experience, cutting-edge infrastructure and carefully designed procedures. We also work continually on developing and establishing new technologies and implement them rapidly into our services.

Struktur der NIG

Our comprehensive lab service covers RNA/DNA preparation, quality control and sample preparation for deep sequencing and microarray analysis. If needed, we also provide researchers with extensive statistical and bioinformatic support ranging from assisting with experimental design to analyzing the generated experimental data.

Our consultation and lab services are open to research groups at the UMG as well as investigators from university and non-university cooperation partners on a cost-sharing basis.

Functional supervision of the core unit lies with Professor Bernd Wollnik, Director of the Institute of Human Genetics. Head of NIG is Dr. Gabriela Salinas.

We look forward to sharing our expertise and capabilities and helping you in your research project. Please contact us to arrange for a consultation or a cost estimate.

Services & Equipment

Request

Contact

Publications

Services & Equipment

Our service portfolio includes initial consultation on project design, sample preparation, molecular analyses and preprocessing of data for further analysis (first-pass data generation).

Leistungen der NIG

Services

Project design planning

An important step to a successful NGS-based experiment is the proper design of a detailed project plan. We aim to optimize the experimental setup to obtain high-quality material and statistical relevance. Together with our users we therefore initially address a number of questions, including:

  • What is the experimental question/hypothesis?
  • How is this experimental question best translated into a statistically relevant and cost effective setup?
  • What is the precise aim of the experiment?
  • What kind of samples should be used and how many of them are necessary to obtain a robust result?
  • How are these samples collected?
  • Which DNA/RNA isolation technique is optimal?
  • How is DNA/RNA integrity achieved?
  • Which platform/technique should be applied?

Next-generation sequencing

Next generation sequencing, or NGS, is a high-throughput approach that allows to analyze base pairs in DNA or RNA samples in a massively parallel fashion. NGS is a powerful tool to address a wide range of research questions. It requires DNA or RNA-based assays and is applied to detect larger genomic variations (e.g. copy number variations) as well as single nucleotide variants. Gene expression analysis, detection of epigenetic variations and molecular analyses including DNA methylation assays are also possible and required. NGS is a driver of discovery and opens the way to personalized medicine.

Microarrays

Our services include various microarray-based applications. Two microarray platforms, the Agilent and the Affymetrix, are available at the NIG. Specifically, we support our users with microarrays for genome expression analysis, exon arrays, miRNA arrays, genotyping and comparative genomic hybridization and SNP arrays.

Data analysis/Bioinformatics

We help researchers in experimental design planning, analysis and generation of publication-ready figures and result interpretation as well as recommendations of follow-up experiments. We support a wide range of NGS applications using both published and in-house developed software programs. Data generation includes quality assessment and optional filtering and trimming of the data. Data analysis includes extensive quality control (QC), mapping, read summarization/SNP calling, data visualization, statistics, functional annotation and interpretation of the data.

In case of leaving standard procedures either for laboratory protocols or statistical analysis and visualization, we would operate on a collaborative basis.

Equipment

We maintain and operate state-of-the art instruments to perform a wide range of analyses in a cost efficient and timely manner.

NGS

  • HiSeq4000
  • HiSeq2500
  • NextSeq
  • MiSeq
  • MinION

Single-cell sequencing

  • C1 System Fluidigm
  • 10 x Genomics
  • CellenONE X1
  • ICELL8 (Takara)

NGS automation and sample quality control

  • Beckman Coulter’s Biomek-automated next-generation sequencing sample prep
  • Fragment Analyzer
  • Pippin prep

Request

We look forward to discussing your specific research project with you. To submit a request, please complete the DNA/RNA sequencing contact form and send it to gsalina@gwdg.de.

Requested analyses will be performed in accordance with the guidelines laid down in the current Nutzerordnung (User Rules and Regulations) and Betriebskonzept (Operational Concept).

Contact

We highly recommend to contact us before starting your project. This will allow us to develop the best possible strategy that meets the demands of genome-wide analysis.

Contact

Dr. Gabriela Salinas
NIG Head

Sample shipment

Please send your samples to:

Dr. Gabriela Salinas
NGS-Integrative Genomics (NIG)
University Medical Center Göttingen (UMG)
Justus-von-Liebig Weg 11
37077 Göttingen

Publications NIG

2019

2018

2017

2016

2015

2014

2019

Sleep Loss Disrupts Morning-to-Evening Differences in Human White Adipose Tissue Transcriptome
Wilms B, Leineweber EM, Mölle M, Chamorro R, Pommerenke C, Salinas-Riester G, Sina C, Lehnert H, Oster H, Schmid SM.
J Clin Endocrinol Metab. 2019 May 1;104(5):1687-1696.

Nuclear Pre-snRNA Export Is an Essential Quality Assurance Mechanism for Functional Spliceosomes
Becker D, Hirsch AG, Bender L, Lingner T, Salinas G, Krebber H.
Cell Rep. 2019 Jun 11;27(11):3199-3214.e3.

Bassoon proteinopathy drives neurodegeneration in multiple sclerosis
Schattling B, Engler JB, Volkmann C, Rothammer N, Woo MS, Petersen M, Winkler I, Kaufmann M, Rosenkranz SC, Fejtova A, Thomas U, Bose A, Bauer S, Träger S, Miller KK, Brück W, Duncan KE, Salinas G, Soba P, Gundelfinger ED, Merkler D, Friese MA.
Nat Neurosci. 2019 Jun;22(6):887-896.

Expression of the DNA-Binding Factor TOX Promotes the Encephalitogenic Potential of Microbe-Induced Autoreactive CD8+ T Cells
Page N, Klimek B, De Roo M, Steinbach K, Soldati H, Lemeille S, Wagner I, Kreutzfeldt M, Di Liberto G, Vincenti I, Lingner T, Salinas G, Brück W, Simons M, Murr R, Kaye J, Zehn D, Pinschewer DD, Merkler D.
Immunity. 2019 Mar 19;50(3):763.

The IL-1 Pathway Is Hyperactive in Hidradenitis Suppurativa and Contributes to Skin Infiltration and Destruction
Witte-Händel E, Wolk K, Tsaousi A, Irmer ML, Mößner R, Shomroni O, Lingner T, Witte K, Kunkel D, Salinas G, Jodl S, Schmidt N, Sterry W, Volk HD, Giamarellos-Bourboulis EJ, Pokrywka A, Döcke WD, Schneider-Burrus S, Sabat R.
J Invest Dermatol. 2019 Jun;139(6):1294-1305.

2018

IL-12 and IL-15 induce the expression of CXCR6 and CD49a on peripheral natural killer cells
Hydes T, Noll A, Salinas-Riester G, Abuhilal M, Armstrong T, Hamady Z, Primrose J, Takhar A, Walter L, Khakoo SI.
Immun Inflamm Dis. 2018 Mar;6(1):34-46.

PI3K: A master regulator of brain metastasis-promoting macrophages/microglia
Blazquez R, Wlochowitz D, Wolff A, Seitz S, Wachter A, Perera-Bel J, Bleckmann A, Beißbarth T, Salinas G, Riemenschneider MJ, Proescholdt M, Evert M, Utpatel K, Siam L, Schatlo B, Balkenhol M, Stadelmann C, Schildhaus HU, Korf U, Reinz E, Wiemann S, Vollmer E, Schulz M, Ritter U, Hanisch UK, Pukrop T.
Glia. 2018 Nov;66(11):2438-2455.

Immortalization of common marmoset monkey fibroblasts by piggyBac transposition of hTERT
Petkov S, Kahland T, Shomroni O, Lingner T, Salinas G, Fuchs S, Debowski K, Behr R.
PLoS One. 2018 Sep 27;13(9):e0204580. doi: 10.1371/journal.pone.0204580. eCollection 2018.

Neurons under T Cell Attack Coordinate Phagocyte-Mediated Synaptic Stripping
Di Liberto G, Pantelyushin S, Kreutzfeldt M, Page N, Musardo S, Coras R, Steinbach K, Vincenti I, Klimek B, Lingner T, Salinas G, Lin-Marq N, Staszewski O, Costa Jordão MJ, Wagner I, Egervari K, Mack M, Bellone C, Blümcke I, Prinz M, Pinschewer DD, Merkler D.
Cell. 2018 Oct 4;175(2):458-471.e19.

Deep phenotyping of human induced pluripotent stem cell-derived atrial and ventricular cardiomyocytes
Cyganek L, Tiburcy M, Sekeres K, Gerstenberg K, Bohnenberger H, Lenz C, Henze S, Stauske M, Salinas G, Zimmermann WH, Hasenfuss G, Guan K.
JCI Insight. 2018 Jun 21;3(12). pii: 99941.

Protein arginine methyltransferase 6 controls erythroid gene expression and differentiation of human CD34+ progenitor cells
Herkt SC, Kuvardina ON, Herglotz J, Schneider L, Meyer A, Pommerenke C, Salinas-Riester G, Seifried E, Bonig H, Lausen J.
Haematologica. 2018 Jan;103(1):18-29

Expression of the DNA-Binding Factor TOX Promotes the Encephalitogenic Potential of Microbe-Induced Autoreactive CD8+ T Cells
Page N, Klimek B, De Roo M, Steinbach K, Soldati H, Lemeille S, Wagner I, Kreutzfeldt M, Di Liberto G, Vincenti I, Lingner T, Salinas G, Brück W, Simons M, Murr R, Kaye J, Zehn D, Pinschewer DD, Merkler D.
Immunity. 2018 May 15;48(5):937-950.e8.

Epithelial-Mesenchymal Transition during Metastasis of HPV-Negative Pharyngeal Squamous Cell Carcinoma
Ihler F, Gratz R, Wolff HA, Weiss BG, Bertlich M, Kitz J, Salinas G, Rave-Fränk M, Canis M.
Biomed Res Int. 2018 Mar 6;2018:7929104.

Effects of repeated long-term psychosocial stress and acute cannabinoid exposure on mouse corticostriatal circuitries: Implications for neuropsychiatric disorders
Tomas-Roig J, Piscitelli F, Gil V, Quintana E, Ramió-Torrentà LL, Del Río JA, Moore TP, Agbemenyah H, Salinas G, Pommerenke C, Lorenzen S, Beißbarth T, Hoyer-Fender S, Di Marzo V, Havemann-Reinecke U.
CNS Neurosci Ther. 2018 Jun;24(6):528-538.

2017

The DNA Methyltransferase 1 (DNMT1) Controls the Shape and Dynamics of Migrating POA-Derived Interneurons Fated for the Murine Cerebral Cortex.
Pensold D, Symmank J, Hahn A, Lingner T, Salinas-Riester G, Downie BR, Ludewig F, Rotzsch A, Haag N, Andreas N, Schubert K, Hübner CA, Pieler T, Zimmer G.
Cereb Cortex. 2017 Dec 1;27(12):5696-5714.

Hepatic gene therapy rescues high-fat diet responses in circadian Clock mutant mice
Meyer-Kovac J, Kolbe I, Ehrhardt L, Leliavski A, Husse J, Salinas G, Lingner T, Tsang AH, Barclay JL, Oster H.
Mol Metab. 2017 Mar 29;6(6):512-523.

The adaptation of colorectal cancer cells when forming metastases in the liver: expression of associated genes and pathways in a mouse model
BBocuk D, Wolff A, Krause P, Salinas G, Bleckmann A, Hackl C, Beissbarth T, Koenig S.
BMC Cancer. 2017 May 19;17(1):342.

The β-catenin/CBP-antagonist ICG-001 inhibits pediatric glioma tumorigenicity in a Wnt-independent manner
Wiese M, Walther N, Diederichs C, Schill F, Monecke S, Salinas G, Sturm D, Pfister SM, Dressel R, Johnsen SA, Kramm CM.
Oncotarget. 2017 Apr 18;8(16):27300-27313.

Histone deacetylase inhibitor MS-275 augments expression of a subset of IFN-γ-regulated genes in Toxoplasma gondii-infected macrophages but does not improve parasite control
Sumpf K, Nast R, Downie B, Salinas G, Lüder CG.
Exp Parasitol. 2017 Feb 9. pii: S0014-4894(17)30083-8.

2016

mRNA quality control is bypassed for immediate export of stress-responsive transcripts
Zander G, Hackmann A, Bender L, Becker D, Lingner T, Salinas G, Krebber H.
Nature. 2016 Dec 12.

The functional readthrough extension of malate dehydrogenase reveals a modification of the genetic code
Hofhuis J, Schueren F, Nötzel C, Lingner T, Gärtner J, Jahn O, Thoms S.
Open Biol. 2016 Nov;6(11).

Pre-Infection Transcript Levels of FAM26F in PBMCS Inform about Overall Plasma Viral Load in Acute and Postacute Phase after SIV-Infection
Javed A, Leuchte N, Salinas G, Opitz L, Stahl-Hennig C, Sopper S, Sauermann U.
J Gen Virol. 2016 Oct 18.

Identification of New Fungal Peroxisomal Matrix Proteins and Revision of the PTS1 Consensus
Nötzel C, Lingner T, Klingenberg H, Thoms S.
Traffic. 2016 Oct;17(10):1110-24

Arc/Arg3.1 governs inflammatory dendritic cell migration from the skin and thereby controls T cell activation
Ufer F, Vargas P, Engler JB, Tintelnot J, Schattling B, Winkler H, Bauer S, Kursawe N, Willing A, Keminer O, Ohana O, Salinas-Riester G, Pless O, Kuhl D, Friese MA.
Sci Immunol. 2016 Sep 23;1(3):eaaf8665.

Treatment of prostate cancer cells with S-adenosylmethionine leads to genome-wide alterations in transcription profiles
Schmidt T, Leha A, Salinas-Riester G.
Gene. 2016 Sep 26. pii: S0378 1119(16)30770-3

The SCN Clock Governs Circadian Transcription Rhythms in Murine Epididymal White Adipose Tissue
Kolbe I, Husse J, Salinas G, Lingner T, Astiz M, Oster H.
J Biol Rhythms. 2016 Sep 20. pii: 0748730416666170

Effects of Long-Term Environmental Enrichment on Anxiety, Memory, Hippocampal Plasticity and Overall Brain Gene Expression in C57BL6 Mice
Hüttenrauch M, Salinas G, Wirths O.
Front Mol Neurosci. 2016 Aug 3;9:62

Prognostic Value of MicroRNAs in Preoperative Treated Rectal Cancer
Azizian A, Epping I, Kramer F, Jo P, Bernhardt M, Kitz J, Salinas G, Wolff HA, Grade M, Beißbarth T, Ghadimi BM, Gaedcke J.
Int J Mol Sci. 2016 Apr 15;17(4):568

The transcriptomes of novel marmoset monkey embryonic stem cell lines reflect distinct genomic features
Debowski K, Drummer C, Lentes J, Cors M, Dressel R, Lingner T, Salinas-Riester G, Fuchs S, Sasaki E, Behr R.
Sci Rep. 2016 Jul 7;6:29122

Physical activity delays hippocampal neurodegeneration and rescues memory deficits in an Alzheimer disease mouse model
Hüttenrauch M, Brauß A, Kurdakova A, Borgers H, Klinker F, Liebetanz D, Salinas-Riester G, Wiltfang J, Klafki HW, Wirths O.
Transl Psychiatry. 2016 May 3;6:e800

MiR144/451 Expression Is Repressed by RUNX1 During Megakaryopoiesis and Disturbed by RUNX1/ETO
DKohrs N, Kolodziej S, Kuvardina ON, Herglotz J, Yillah J, Herkt S, Piechatzek A, Salinas Riester G, Lingner T, Wichmann C, Bonig H, Seifried E, Platzbecker U, Medyouf H, Grez M, Lausen J.
PLoS Genet. 2016 Mar 18;12(3):e1005946

The Cannabinoid CB1/CB2 Agonist WIN55212.2 Promotes Oligodendrocyte Differentiation In Vitro and Neuroprotection During the Cuprizone-Induced Central Nervous System Demyelination
Tomas-Roig J, Wirths O, Salinas-Riester G, Havemann-Reinecke U.
CNS Neurosci Ther. 2016 May; 22(5):387-95

Social defeat leads to changes in the endocannabinoid system: An overexpression of calreticulin and motor impairment in mice
Tomas-Roig J, Piscitelli F, Gil V, Del Río JA, Moore TP, Agbemenyah H, Salinas-Riester G, Pommerenke C, Lorenzen S, Beißbarth T, Hoyer-Fender S, Di Marzo V, Havemann-Reinecke U.
Behav Brain Res. 2016 Apr 15;303:34-43

Short-Term Molecular Acclimation Processes of Legume Nodules to Increased External Oxygen Concentration
Avenhaus U, Cabeza RA, Liese R, Lingner A, Dittert K, Salinas-Riester G, Pommerenke C, Schulze J.
Front Plant Sci. 2016 Jan 6;6:1133. doi: 10.3389/fpls.2015.01133. eCollection 2015

CD14 is a key organizer of microglial responses to CNS infection and injury
Janova H, Böttcher C, Holtman IR, Regen T, van Rossum D, Götz A, Ernst AS, Fritsche C, Gertig U, Saiepour N, Gronke K, Wrzos C, Ribes S, Rolfes S, Weinstein J, Ehrenreich H, Pukrop T, Kopatz J, Stadelmann C, Salinas-Riester G, Weber MS, Prinz M, Brück W, Eggen BJ, Boddeke HW, Priller J, Hanisch UK.
Glia. 2016 Apr;64(4):635-49

Long-Term Oocyte-Like Cell Development in Cultures Derived from Neonatal Marmoset Monkey Ovary
Fereydouni B, Salinas-Riester G, Heistermann M, Dressel R, Lewerich L, Drummer C, Behr R.
Stem Cells Int. 2016;2016:2480298

Modulation of CNS autoimmune responses by CD8(+) T cells coincides with their oligoclonal expansion
Fischer HJ, van den Brandt J, Lingner T, Odoardi F, Flügel A, Weishaupt A, Reichardt HM.
J Neuroimmunol. 2016 Jan 15;290:26-32

Microarray analysis of circulating micro RNAs in the serum of patients with polymyositis and dermatomyositis reveals a distinct disease expression profile and is associated with disease activity
Misunova M, Salinas-Riester G, Luthin S, Pommerenke C, Husakova M, Zavada J, Klein M, Plestilova L, Svitalkova T, Cepek P, Novota P, Vencovsky J.
Clin Exp Rheumatol. 2016 Jan-Feb;34(1):17-24. Epub 2015 Nov 17

2015

SMRT sequencing of the Campylobacter coli BfR-CA-9557 genome sequence reveals unique methylation motifs
Zautner AE, Goldschmidt AM, Thürmer A, Schuldes J, Bader O, Lugert R, Groß U, Stingl K, Salinas G, Lingner T.
BMC Genomics. 2015 Dec 21;16:1088

Global analysis of asymmetric RNA enrichment in oocytes reveals low conservation between closely related Xenopus species
Claußen M, Lingner T, Pommerenke C, Opitz L, Salinas G, Pieler T.
Mol Biol Cell. 2015 Nov 1;26(21):3777-87

Thymocyte-derived BDNF influences T-cell maturation at the DN3/DN4 transition stage
Linker RA, Lee DH, Flach AC, Litke T, van den Brandt J, Reichardt HM, Lingner T, Bommhardt U, Sendtner M, Gold R, Flügel A, Lühder F.
Eur J Immunol. 2015 May;45(5):1326-38

Central role of Th2/Tc2 lymphocytes in pattern II multiple sclerosis lesions
Planas R, Metz I, Ortiz Y, Vilarrasa N, Jelčić I, Salinas-Riester G, Heesen C, Brück W, Martin R, Sospedra M.
Ann Clin Transl Neurol. 2015 Sep;2(9):875-93

Influence of total genomic alteration and chromosomal fragmentation on response to a combination of azacitidine and lenalidomide in a cohort of patients with very high risk MDS
Ganster C, Shirneshan K, Salinas-Riester G, Braulke F, Schanz J, Platzbecker U, Haase D.
Leuk Res. 2015 Oct;39(10):1079-87

Sensing Cardiac Electrical Activity With a Cardiac Myocyte-Targeted Optogenetic Voltage Indicator
Chang Liao ML, de Boer TP, Mutoh H, Raad N, Richter C, Wagner E, Downie BR, Unsöld B, Arooj I, Streckfuss-Bömeke K, Döker S, Luther S, Guan K, Wagner S, Lehnart SE, Maier LS, Stühmer W, Wettwer E, van Veen T, Morlock MM, Knöpfel T, Zimmermann WH.
Circ Res. 2015 Aug 14;117(5):401-12

Next generation sequencing of sex-specific genes in the livers of obese ZSF1 rats
Babelova A, Burckhardt BC, Salinas-Riester G, Pommerenke C, Burckhardt G, Henjakovic M.
Genomics. 2015 Jul 19. pii: S0888-7543(15) 30021-5

The oxidative demethylase ALKBH3 marks hyperactive gene promoters in human cancer cells
Liefke R, Windhof-Jaidhauser IM, Gaedcke J, Salinas-Riester G, Wu F, Ghadimi M, Dango S.
Genome Med. 2015 Jun 30;7(1):66

Thymocyte-derived BDNF influences T-cell maturation at the DN3/DN4 transition stage
Linker RA, Lee DH, Flach AC, Litke T, van den Brandt J, Reichardt HM, Lingner T, Bommhardt U, Sendtner M, Gold R, Flügel A, Lühder F.
Eur J Immunol. 2015 May;45(5):1326-38

Destabilization of pluripotency in the absence of Mad2l2
Pirouz M, Rahjouei A, Shamsi F, Eckermann KN, Salinas-Riester G, Pommerenke C, Kessel M.
Cell Cycle. 2015 Apr 30:0

Overexpression of mutant Ptch in rhabdomyosarcomas is associated with promoter hypomethylation and increased Gli1 and H3K4me3 occupancy
Nitzki F, Tolosa EJ, Cuvelier N, Frommhold A, Salinas-Riester G, Johnsen SA, Fernandez-Zapico ME, Hahn H.
Oncotarget. 2015 Apr 20;6(11):9113-24

Non-viral generation of marmoset monkey iPS cells by a six-factor-in-one-vector approach
Debowski K, Warthemann R, Lentes J, Salinas-Riester G, Dressel R, Langenstroth D, Gromoll J, Sasaki E, Behr R.
PLoS One. 2015 Mar 18;10(3):e0118424

mRNA profiling reveals determinants of trastuzumab efficiency in HER2-positive breast cancer
von der Heyde S, Wagner S, Czerny A, Nietert M, Ludewig F, Salinas-Riester G, Arlt D, Beißbarth T.
PLoS One. 2015 Feb 24;10(2):e0117818

2014

Integrated miRNA and mRNA profiling of tumor-educated macrophages identifies prognostic subgroups in estrogen receptor-positive breast cancer
Bleckmann A, Leha A, Artman S, Menk K, Salinas-Riester G, Binder C, Pukrop T, Beissbarth T, Klemm F.
Mol Oncol. 2014 Aug 16. pii: S1574-7891(14)00178-1

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