The Penn State Hershey Genome Sciences Facility is a full service facility and provides consultation, instrumentation, and services to both Penn State and non-Penn State investigators in genomic, epigenomic, and transcriptomic studies (http://www.pennstatehershey.org/web/core/gene-expression-analysis-overview). The variety of instrumentation allows for capabilities ranging from highly focused analysis of candidate SNPs and mRNAs to whole genome, exome, epigenome, and transcriptome sequencing. Services are also available for a variety of study designs extending from a few laboratory samples to large (100s to 1,000s of samples) clinical projects. The full bioinformatics service is also available for data analysis.  

The Facility resides in 5,000 sq ft of newly renovated space, encompassing separate "pre-amplification" and "post-amplification" rooms to prevent any contamination of PCR-amplified materials to pre-processed input DNA/RNA samples. Four well-experienced staff members are available for assisting in project operations. In addition, the lab space is available for investigators who need temporary room for sample preparation.

We receive either tissue, DNA/RNA, or customer-generated NGS libraries. We process samples according based on agreement reached during consultations on the design of the experiment. We develop new applications to accommodate state-of-the-art NGS technologies. We conduct sequence read alignment, secondary analysis  (quantitation, variant calling, functional annotation, visualization, etc) and follow-up with the interpretation of the results. We provide support for grant writing and hands-on training for students and post-docs in NGS processing. 

Please contact Director (Yuka Imamura, 717-531-0003 ext.289250) for more information (http://sites.psu.edu/yuka/)

NEW: Facebook: https://www.facebook.com/gsfpsucomservice

Instrumentation

Sample processing

Sample quantitation and quality control

qPCR/Digital PCR
Microarray analyses

Next Generation Sequencing (NGS)

Other DNA Sequencing
Software
  • Agilent Genespring:  Please contact Research Computing for information on IPA and Genespring
  • Illumina GenomeStudio
  • Illumina iCompute
  • Ingenuity Pathway Analysis: Please contact Research Computing for information on IPA and Genespring
Additionally the facility contains refrigerators, -20ºC and -80ºC freezers, and associated small equipment (e.g. multichannel, electronic, and accordion pipettes, centrifuges, etc.).

Nucleic Acid Isolation 

Nucleic acid isolation is available using the QIAsymphony DNA/RNA Extraction Robot.  The QIAsymphony SP enables sample preparation of DNA, RNA, bacterial and viral nucleic acids from whole blood, saliva and buffy coat among other sample types. 

Available preps:

200 ul Whole Blood DNA prep
400 ul Whole Blood  DNA prep
1000 ul Whole Blood DNA prep
200 ul DNA prep buffy coat
400 ul DNA prep buffy coat
400 ul RNA prep
800 ul RNA prep
PAXgene_RNA
1000 ul Saliva DNA prep 

For more information and cost estimate of project, please contact Sue Patrick x5676  sdp8@psu.edu

Covaris Adaptive Focused Acoustics Ultrasonicator providing DNA and chromatin shearing capabilities, is available in room C2706.  The Covaris enables shearing of samples without thermal damage.  The equipment is available on a sign-up basis. For additional information and cost estimate of project, please contact Sue Patrick x5676 sdp8@psu.edu.

 

NextGen/Whole Genome Sequencing 

Genome Sciences has Illumina sequencing instrumentation (MiSeq and HiSeq 2500) for both focused and large-scale sequencing by synthesis. MiSeq and HiSeq 2500  services are available. Specific library construction services are available. Contact Genome Sciences staff at x5823 or by email ( preferred - see Contact page ) for more information.

MiSeq:
For library construction we recommend Illumina library preparation kits, and most other library preparation kits with Illumina adaptors will work with the MiSeq. To aid in choosing the appropriate library construction kit see our compatibility chart. If you have a sequencing project please consult Genome Sciences staff before submitting samples and to obtain costs.  
 
 
HiSeq 2500:
Both rapid run and high output workflows are now available on the HiSeq2500.
 
 
Please contact Rob Brucklacher  531-5823 rbrucklacher@hmc.psu.edufor cost estimate of project(s).
 

NextGen Sequencing Library Prep

We provide a variety of library preparation services including whole genome, whole exome, ChIP-seq, Methylation-seq, RNA-seq and targeted resequencing. Listed below are currently operated services, but we are expanding the service to meet the needs of each investigator.

 NGS Library Prep Service

For more information and cost estimate of service, please contact

Yuka Imamura 717-531-0003 x289250  yimamura@hmc.psu.edu

 
 Whole Genome Sequencing library prep
 Whole Exome Sequencing (Human) (minimum input DNA 1 ng for intact DNA, under R&D  for FFPE DNA)
 Exome (other species, mouse, bovine, zebrafish)
 ChIP-sequencing library prep (minimum input DNA 0.5 ng)
 Low input ChIP-seq library prep (minimum input DNA 0.05 ng)
 Methylation sequencing -ERRBS (enhanced reduced representation of bisulfite  sequencing) library prep
 PolyA RNA seq library prep (strand-specific, minimum input RNA 50 ng)
 Total RNA seq library prep (rRNA depleted, human, mouse, rat, standard rRNA-depletion,  strand-specific, minimum input RNA 100 ng)
 Low Input RNA-seq library prep (minimum input RNA 10 pg, or single cell)
 Low Input cDNA synthesis (minimum input RNA 10 pg, or single cell)
 Degraded Low Input RNA-seq library prep (minimum input RNA 10 ng)
 Degraded Low Input cDNA synthesis
 Small RNA seq library prep (minimum input RNA 1 ug)
 Low input small RNA-seq library prep (minimum input RNA 100 ng)
 Single cel RNA-seq (up to 96 samples)

*QC bioanalyzer run will be added (usually 3 runs with up to 11 samples per chip)

The Molecular Genetics Core Facility (MGCF)  is now a part of Genome Sciences and is located in C2705.  We can provide custom DNA sequencing centered around an ABI 3130XL Capillary sequencer.

The Genome Sciences Facility also provides genotyping, SNPlex analysis and fragment analysis.

DNA Sequencing Order Sheet Instructions

DNA Sequencing order sheet is now an .xls spread sheet.   A copy of the Submission form may be found at the network pathway \\hersheymed.net\files\research\corefacility\Results\DNA-Sanger Sequencing.  

Please save completed Submission forms in the same network folder.

Least preferred but acceptable submission is email to either rmb6@psu.edu or gvp103@psu.edu.

Template ID: use the laboratory P.I.'s initials and then number each DNA sample sequentially with every submission, e.g. JS10, JS11, JS12 etc. The template ID should also be used to label the tube of DNA submitted, on the top of each tube. If the same DNA is being tested with more than one primer, you may put the DNA in a single tube, but it must be labeled with more than one Template ID number, e.g. JS10-13

**Template concentration: SAMPLES MUST BE IN WATER. For PLASMID and BAC samples, the DNA concentration should be ~100ng/µl - please submit 800ng (=8 µl at 100ng/µl) of DNA per sequencing reactionFor PCR products, the DNA concentration should be ~10 ng/µl, and 5ng PCR product DNA/100bases length should be submitted. Please indicate SIZE of the PCR product in the Template size column above; also indicate in the Notes column that the template is PCR product.

Primer Name: Indicate here the name of the primer to be used for sequencing. Concentrations should be 5-10uM. The Core Facility provides at no charge common primers such as T7, T3, SP6, etc.

If you are using your own primer(s), the Tm should be between 55 and 60°C; thus, the length should be approximately 18-25 nucleotides. The core uses the following equation to estimate Tm: Tm = 2°C X (A + T) + 4°C X (G + C).

Notes: should be used for three purposes: 1) you may write your own notes for reference here, 2) request any special reaction conditions required e.g. DMSO to minimize 2° structure in GC rich templates, 3) indicate if the DNA template is anything other than plasmid DNA, e.g. BAC, PCR product, etc.(for BAC or PAC samples provide either primer Tm or actual sequence for Tm determination).

DNA Sequencing - Standard Primers Available

BGH Reverse:  5' -d(TAG AAG GCA CAG TCG AGG C)
GL primer 2:  5' -d(TTT ATG TTT TTG GCG TCT TCC)
RV3:  5' -d(AGT GCA AGT GCA GGT GCC AGA)
M13 forward (-21):  5' -d(TGT AAA ACG ACG GCC AG)
M13 reverse:  5' -d(CAG GAA ACA GCT ATG ACC)
SP6 promoter:  5' -d(ATT TAG GTG ACA CTA TA)
T3 promoter:  5' -d(AAT TAA CCC TCA CTA AAG GG)
T7 promoter:  5' -d(TAA TAC GAC TCA CTA TAG GG)
T7 terminator:  5' -d(GCT AGT TAT TGC TCA GCG G)

 

Sample QA\QC

RNA Quality Assessment

Note: All RNA (total or mRNA/poly-A+) must be assessed for quality ("QCed") before use in array analysis. It is also recommended prior to any applications, as good quality RNA is the foundation of all subsequent work and you want to insure that you have quality and validity to your experiments.

  • At least 3 µl of RNA at a concentration > 0.1-0.5 µg/µl must be provided in a well-labeled tube for the quality control analysis.
  • RNA QC  for up to 12 samples analyzed on RNA 6000 Nano chip and up to 11 samples analyzed for the RNA 6000 Pico chip (rare or micro-dissected samples).

 

 

Image of Perfect RNA - image of partially digested RNA -- image of severely degraded -- image of genomic DNA contaminated RNA

Acknowledgement and thanks for the Bioanalyzer images used

Protocols:

Links to additional protocols will be added as warranted.

Good information - An RNA Primer

We have found the Trizol/Tri-Reagent RNA Isolation Protocol to work well for many sample types.

Qiagen RNeasy kit is another preferred RNA isolation method and is available in the Core Supply Center (C1733).


RNA & DNA QC samples

RNA QC Samples to be submitted by filling out the proper form (RNA Nano, Pico ) or DNA located at

\\hersheymed\files\Research\CoreFacility\Results\Functional Genomics Incoming

and saving into the Functional Genomics Incoming QC Submission Folder on the network drive

\\hersheymed\files\Research\CoreFacility\Results\Functional Genomics Incoming\~QC Submissions.

NOTE: Nano chips hold 12 samples. Pico chips hold 11.

Map your network to this address:

\\hersheymed\files\Research\CoreFacility\Results\Functional Genomics Incoming   and into the QC Incoming folder

Please use the Excel form  and File Save As _ into the folder above.

DNA samples are submitted following the same guidelines.

Samples are to be put in the freezer in C2705A in the Genome Sciences QC (Bioanalyzer) box. The freezer is marked with a Genome Sciences Dropoff sign.

Note: Use your Name or other Unique description and please make sure the tubes are labeled with something descriptive, as well.

All incoming files to be saved into subfolders in the following folder:

\\hersheymed\files\Research\CoreFacility\Results\Functional Genomics Incoming

Completed results of all work are put in individual researcher folders located at

\\hersheymed\files\Research\CoreFacility\Results\Functional Genomics

qPCR

Please remember to check News & Events and the Calendar for up-to-date information.

Quantitative Real-Time PCR

 

QuantStudio 12KFlex with 384-well, 96-well and available OpenArray block is in C2705.

Please schedule your run if using 96-well plate project, as our usual block is the 384-well plate block.

384-well barcoded plates and seals may be purchased in the Supply Center.

You may call  x5823 or (preferred) email Rob  or Georgina for instructions.

You may still use SDS software to create the plate and  export the setup file into the "Incoming 7900 Plates" folder in the network folder located here:

\\hersheymed\files\Research\CoreFacility\Results\Functional Genomics Incoming

Note:  File - Export setup, not the SDS file itself.

 

QuantStudio licenses are also available for purchase  through the core.

 

Analysis for Comparative Ct plates (RQ) can be done in your lab using free ExpressionSuite software from LifeTechnologies.

 

 

Quantitative Real-Time PCR is used to very precisely measure the amount of gene expression in cells or tissue of interest, relative to an endogenous control gene such as 18s, b-actin, etc. The two major methods to perform QRTPCR that are supported here in the Functional Genomics Core Facility are dual-labeled probe chemistry (TAQMAN®) and SYBR green chemistry.

Our recommendation for ease of use is to utilize the pre-optimized Primer/Probe Applied Biosystems Gene Expression Assays ( aka Assays-on-Demand ). These may be ordered through the Core Facility.

We can assist in finding other sources should your gene not be available at ABI, either with another company or with design assistance ( see below on this page ).

A very good source of information describing techniques and including troubleshooting may be found in the 2006 GenomeTech-RT-PCR TechGuide

A brief description ( of both Taqman 5'-nuclease ( dual-labelled probe chemistry ) and SYBR green ) follows:

Taqman Dual-Labeled Probe ( 5'-nuclease )

An oligo that is complementary to a portion of your gene of interest sequence between your PCR primers. This oligo has an fluor attached to the 5' end, and a quencher attached to the 3' end. When the oligo has hybridized to your gene sequence, and the polymerase incorporates it into the new product, the fluor is allowed to distance itself from the quencher. The rate at which new copies of your gene of interest are generated is inferred by the rate at which the intensity of this free fluor increases.

Dual labeled probes are more specific than SYBR green because dual labeled probe chemistry requires specific amplification of the gene of interest in order for fluorescence to be generated. SYBR Green, however, will generate fluorescent signal in the cases of mispriming and the formation of primer dimers. In addition, two different genes of interest may be amplified in one reaction, and detected independently from one another by using different fluors one each dual labeled probe. The disadvantage of using dual-labeled probes is that one dual-labeled probe must be purchase for each gene of interest.

SYBR Green

A dye that will bind to double stranded nucleic acid. As your primers anneal and the polymerase extends to make new copies of your gene of interest, the amount of SYBR green increases proportionately. The rate at which new copies of your gene of interest are generated is inferred by the rate at which SYBR green fluorescence increases.

Should you be using an unavailable species and/or your gene is not yet listed we are also available to assist with Primer Design and Purchase.

A frequently updated list of validated primer/probe sets for quantitation of a variety of mRNAs is maintained at http://www.realtimeprimers.org/

To design your own primer/probe sets, you can use Primer Express, which is available in our facility (C2705).

Contact Rob Brucklacher  (x5823) for more information and assistance.

Flanking 5' (forward) and 3' (reverse) Primers can be made in our Macromolecular Core Facility -- or through external companies such as IDTDNA, Invitrogen, Applied Biosystems, etc.

Microarrays

 Gene Expression Microarrays

The Genome Sciences Core uses the Illumina platform which comes in several formats

·         Mouse Whole Genome Array (multiple of 6, minimum available for purchase is 12).

·         Mouse RefSeq8 Array (multiples of 8, minimum available for purchase is 16, only sequences are RefSeq ).

·         Human HT_12 arrays (multiples of 12, minimum available for purchase is 24 ).

Genotyping Microarrays

·         For focused genotyping/CNV/Methylation studies the Infinium or GoldenGate process using the iScan instrument is extremely powerful. This platform allows investigators to choose a wide variety for specific research aims. 

Contact  Core staff for more information and cost estimates for project by email .

 

Recent Publications

  1. Imamura Kawasawa, Y., Salzberg, A.C., Li, M., Sestan, N., Greer, C.A., Imamura, F. Genome-wide transcriptome analysis of developing olfactory bulb projection neurons (in revision)
  2. Popova, E.Y., Pinzon-Guzman, C., Salzberg, A.C., Zhang, S.S., Barnstable, C.J. LSD1-mediated demethylation of H3K4me2 is required for the transition from late progenitor to differentiated mouse rod photoreceptor. Molecular Neurobiology 2015 Aug 23. [Epub ahead of print] PMID: 26298666
  3. Ge Z, Guo X, Li J, Hartman M, Kawasawa YI, Dovat S, Song C. Clinical significance of high c-MYC and low MYCBP2 expression and their association with Ikaros dysfunction in adult acute lymphoblastic leukemia. Oncotarget. 2015 Dec 8; 6(39):42300-11.
  4. Govey PM, Kawasawa YI, Donahue HJ. Mapping the osteocytic cell response to fluid flow using RNA-Seq. J Biomech. 2015 Dec 16; 48(16):4327-32.
  5. He F, Bixler EO, Liao J, Berg A, Imamura Kawasawa Y, Fernandez-Mendoza J, Vgontzas AN, Liao D. Habitual sleep variability, mediated by nutrition intake, is associated with abdominal obesity in adolescents. Sleep Med. 2015 Dec; 16(12):1489-94.
  6. Lynch CJ, Kimball SR, Xu Y, Salzberg AC, Kawasawa YI. Global deletion of BCATm increases expression of skeletal muscle genes associated with protein turnover. Physiol Genomics. 2015 Nov; 47(11):569-80.
  7. Clawson GA, Matters GL, Xin P, Imamura-Kawasawa Y, Du Z, Thiboutot DM, Helm KF, Neves RI, Abraham T. Macrophage-Tumor Cell Fusions from Peripheral Blood of Melanoma Patients. PLoS One. 2015; 10(8):e0134320.
  8. Lynch CJ, Xu Y, Hajnal A, Salzberg AC, Kawasawa YI. RNA sequencing reveals a slow to fast muscle fiber type transition after olanzapine infusion in rats. PLoS One. 2015; 10(4):e0123966.
  9. He F, Bixler EO, Berg A, Imamura Kawasawa Y, Vgontzas AN, Fernandez-Mendoza J, Yanosky J, Liao D. Habitual sleep variability, not sleep duration, is associated with caloric intake in adolescents. Sleep Med. 2015 Jul; 16(7):856-61.
  10. Berry, G.J., Frielle, C.M., Brucklacher, R.M., Salzberg, A.C., Waldner, H. Identifying type 1 diabetes candidate genes by DNA microarray analysis of islet-specific CD4+ T cells Genomics Data 5:184-188 (2015)
  11. Robey, R.B., … Salzberg, A.C., … et al. Metabolic Reprogramming and Dysregulated Metabolism in Cancer: Pleiomorphic Mechanistic Targets, Antagonists, and Enablers of Complex Low Dose Environmental Exposures? Carcinogenesis 36(S1):S203-S231 (2015)
  12. Goodson III, W.H., … Salzberg, A.C., … et al. Assessing the Carcinogenic Potential of Low Dose Exposures to Chemical Mixtures in the Environment: The Challenge Ahead Carcinogenesis 36(S1):S254-S296 (2015)
  13. Berry, G.J., Frielle, C., Luu, T., Salzberg, A.C., Rainbow, D.B., Wicker, L.S., Waldner, H. Genome-wide transcriptional analyses of islet-specific CD4+ T cells identify Idd9 genes controlling diabetogenic T cell function. J. Immunology 194(6):2654-63 (2015)
  14. Wilson, R.T., Borner, J.D., Roff, A., Das, A., Richie, J.P., Bamholtz-Sloan, J., Chinchilli, V.M., Berg, A., Liu, G., Salzberg, A.C., El-Bayoumy, K. Genetic and Environmental Influences on Plasma Vitamin D Binding Protein Concetrations.  Translational Research165(6):667-676 (2015)
  15. He F, Rodriguez-Colon S, Fernandez-Mendoza J, Vgontzas AN, Bixler EO, Berg A, Imamura Kawasawa Y, Sawyer MD, Liao D. Abdominal obesity and metabolic syndrome burden in adolescents-penn state children cohort study. J Clin Densitom. 2015 Jan; 18(1):30-6.
  16. Chen SJ, Hoffman NE, Shanmughapriya S, Bao L, Keefer K, Conrad K, Merali S, Takahashi Y, Abraham T, Hirschler-Laszkiewicz I, Wang J, Zhang XQ, Song J, Barrero C, Shi Y, Kawasawa YI, Bayerl M, Sun T, Barbour M, Wang HG, Madesh M, Cheung JY, Miller BA. A Splice Variant of the Human Ion Channel TRPM2 Modulates Neuroblastoma Tumor Growth through Hypoxia-inducible Factor (HIF)-1/2a. J Biol Chem. 2014 Dec 26; 289(52):36284-302.
  17. Rodríguez-Colón S, He F, Bixler EO, Fernandez-Mendoza J, Vgontzas AN, Berg A, Kawasawa YI, Liao D. The circadian pattern of cardiac autonomic modulation and obesity in adolescents. Clin Auton Res. 2014 Dec; 24(6):265-73.
  18. Fertuzinhos S, Li M, Kawasawa YI, Ivic V, Franjic D, Singh D, Crair M, Sestan N. Laminar and temporal expression dynamics of coding and noncoding RNAs in the mouse neocortex. Cell Rep. 2014 Mar 13; 6(5):938-50.
  19. Dluzen, D., Sun, D., Salzberg, A.C., Jones, N., Bushey, R., Robertson, G., Lazarus, P. Regulation of UGT1A1 expression and activity by miR-491-3p. JPET, 113.210658 (2014)
  20. Pletikos M, Sousa AM, Sedmak G, Meyer KA, Zhu Y, Cheng F, Li M, Kawasawa YI, Sestan N. Temporal specification and bilaterality of human neocortical topographic gene expression. Neuron. 2014 Jan 22; 81(2):321-32.
  21. Popova, E.Y., Xu, X., DeWan, A.T.,.Salzberg, A.C., Berg, A., Hoh, J., Zhang, S.S., Barnstable, C.J. Stage and Gene Specific Signatures Defined by Histones H3K4me2 and H3K27me3 Accompany Mammalian Retina Maturation in Vivo.  PLoS ONE7(10):e46867 (2012)
  22. Qi, J., Rice, S.J., Salzberg, A.C., Liao, J., Zander, D.S., and Mu, D. MiR-365 Regulates Lung Cancer and Developmental Gene Thyroid Transcription Factor 1. Cell Cycle , 11(1), 177-186 (2012)
  23. Kang HJ, Kawasawa YI, Cheng F, Zhu Y, Xu X, Li M, Sousa AM, Pletikos M, Meyer KA, Sedmak G, Guennel T, Shin Y, Johnson MB, Krsnik Z, Mayer S, Fertuzinhos S, Umlauf S, Lisgo SN, Vortmeyer A, Weinberger DR, Mane S, Hyde TM, Huttner A, Reimers M, Kleinman JE, Sestan N. Spatio-temporal transcriptome of the human brain. Nature. 2011 Oct 27; 478(7370):483-9.
  24. Hashimoto-Torii K, Kawasawa YI, Kuhn A, Rakic P. Combined transcriptome analysis of fetal human and mouse cerebral cortex exposed to alcohol. Proc Natl Acad Sci U S A. 2011 Mar 8; 108(10):4212-7.
  25. Freeman, W.M., Salzberg, A.C., Gonzales, S.W., Grant, K.A., Vrana, K.E. Classification of alcohol abuse by plasma protein biomarkers. Biol Psychiatry, 68(3), 219-222 (2010)

Recent Conference Abstracts

  1. Hiroko Shike , Zakiyah Kadry, Riaz Shah, Yuka Imamura, Wallace Greene, Justine Gaspari, Thomas Riely, Howard Nathan, Richard Hasz, Ashokkumar Jain. Quantitative Hepatitis C Virus (HCV) RNA in Plasma and Kidney Tissue in HCV Antibody Positive Donors. American Transplant Congress (2016)
  2. Amanda Nelson, Brian Kidd, Yuka Imamura Kawasawa, Joel Dudley, Diane Thiboutot. Isolating and Identifying the Acne Skin Microbiome. Society of Investigative Dermatology Meeting (2016)
  3. Peter M. Govey, Yuka Imamura Kawasawa, Henry J. Donahue. Mapping the Osteocytic Cell Response to Fluid Flow Using RNA-Seq. Orthopaedic Research Society (2016)
  4. Sun, Y., El-Bayoumy, K., Imamura, Y., Salzberg, A., Aliaga, C., Gowdahalli, K., Amin, S., Chen, K. Genome-wide analysis of DNA methylation induced by environmental carcinogen dibenzo[def,p]chrysene in ovarian tissues of mice.  AACR, (2016)
  5. Christine S. Choi, Yuka Imamura Kawasawa, Gregory S. Yochum, Leonard R. Harris, Sue M. Deiling, Walter A. Koltun. Attenuated Expression of Nuclear Receptor Family NR4A in Familial Diverticulitis. Presentation at Academic Surgical Congress, (2016)
  6. Lee, S.Y., Zhu, J., Salzberg, A., Liu, D.J., Connor, J.R. Association study between HFE polymorphisms and survival of glioblastoma patients in TCGA database.  Neuro Oncol(suppl 5): v82 (2015)
  7. Weisz, J., Shearer, D., Salzberg, A. Adaptation to chronic oxidative stress (OxS) during latent states of carcinogenesis: an evolutionary complex adaptive system based model of breast carcinogenesis.   of International Society of Antioxidants in Health & Nutrition1(1) (2015)
  8. Popova, E., Pinzon-Guzman, C., Salzberg, A., Hass, D., Zhang, S.S., Barnstable, C.J. The role of Lysine demethylase 1 in mouse rod photoreceptor development and maturation. Investigative Ophthalmology & Visual Science56(7):438 (2015)
  9. Sun, Y., Chen, K., Imamura Kawasawa, Y., Salzberg, A., Aliaga, C., Gowdahalli, K., Amin, S., Stoner, G., El-Bayoumy, K. The effects of the environmental carcinogen dibenzo[a,l]pyrene on genome-wide methylation and the impact of dietary black raspberry in mouse oral tissues. Cancer Research75 (15 Supplement), 2955-2955 (2015).
  10. Weisz, J., Shearer, D., Salzberg, A.C. Using reduction mammoplasty tissues from healthy young women living in USA’s high breast cancer (BC) risk posing environment to open up to study the “black box” of latent stages of breast carcinogenesis: a key to develop strategies for BC prevention.  Cancer Research75 (15 Supplement), 4558-4558 (2015).
  11. Berg, A., Imamura Kawasawa, Y., Salzberg, A., Bixler, E.O., He, F., Liao, D. Abstract P260: Obesity is associated with DNA Methylation in Population-Based Adolescents. Circulation 131 (Suppl 1), AP260-AP260 (2015)
  12. Rodriguez-Colon, S.M., Berg, A., Imamura Kawasawa, Y., Salzberg A., Bixler, E.O., Fernandez-Mendoza, J., Vgontzas, A.N, Liao, D. Abstract MP91: Abdominal Obesity, Independent of General Obesity, is Associated With Reduced Circadian Pattern of Cardiac Autonomic Modulation in Adolescents. Circulation 131 (Suppl 1), AMP91-AMP91 (2015)
  13. Popova, E., Pinzon-Guzman, C., Salzberg, A., Berg, A., Zhang, S.S., Barnstable, C.J. Lysine demethylase 1 is required for mouse rod photoreceptor development. Investigative Ophthalmology & Visual Science55(13):4998-4998 (2014)
  14. Waldner, H., Berry, G., Frielle, C., Salzberg, A.C. Identification of candidate genes for type 1 diabetes by microarray expression analysis of islet-specific CD4+ T cells (IRM6P.726). The Journal of Immunology192 (1 Supplement), 63.18-63.18 (2014)
  15. Lehman, H., Welsh, P., Mass, J., Salzberg, A., Berg, A., Stairs, D. Investigating the mechanisms of esophageal squamous cell carcinoma invasion (59.9).  The FASEB Journal 28 (1 Supplement), 59.9 (2014)
  16. Grigoryev, S., Salzberg, A.C., Berg, A., Harris-Becker, A., Loughran, T., Claxton, D. Genome-wide mapping of large organized heterochromatin domains reveals hotspots of epigenetic and transcriptional changes associated with myeloid differentiation and acute myeloid leukemia (565.1). The FASEB Journal28 (1 Supplement), 565.1 (2014)
  17. Archibeque, L.D., Barnholtz-Sloan, J., Battaglioli, E.J., Salzberg, A.C., Wilson, R.T. Polymorphisms in CYP24A1 and CYP3A43: possible effect modification by the vitamin D binding protein and vitamin D receptor. American Institute for Cancer Research. November, 2013.
  18. Spratt, T.E., Gowda, A.S., Salzberg, A., Berg, A., Song, C., Dovat, S.S. Binding of benzo[a]pyrene diol epoxide to the genome. Abstracts of Papers of the American Chemical Society246 (2013)
  19. Dluzen, D.F., Salzberg, A., Sun, D., Jones, N., Bushey, R., Lazarus, P. miR-491-3p regulation of the UDP-glucuronosyltransferase (UGT) 1A gene family. Cancer Research73 (8) (2013)
  20. MacNeill, C; Salzberg, A.C.; Phelps, D.S; Umstead, T.M.; Floros, J.; Weisz, J. Proteomic Studies of Vestibular Swab Extracts Identify Reduced Levels of Serine Protease Inhibitors in Patients with Vulvodynia. ISSVD XXII World Congress. October, 2013.
  21. Qi, J; Rice, S.J.; Salzberg, A.C.; Runkle, A.; Liao, J.; Zander, D.S.; Mu, D.  MiR-365 regulates lung cancer and developmental gene TTF-1. Cancer Research72 (8 Supplement), 2307-2307 (2012)

Calendar

For experimental scheduling and Core closures please see:

http://genomics.calendarhost.com/cgi-bin/calweb/calweb.cgi

Contact

The Genome Sciences Core is located in C2705.

Director

Yuka Imamura Kawasawa, Ph.D

Email: yimamura@hmc.psu.edu
Phone: 717-531-0003 x289250

Staff

Robert Brucklacher
Email:  rbrucklacher@hmc.psu.edu
Phone: 717-531-5823

Georgina Bixler
Email: gbixler2@hmc.psu.edu
Phone: 717-531-5823

Elizabeth Conroy
Email: econroy@hmc.psu.edu 
Phone: 717-531-4699

Anna Salzberg
Email: asalzberg@hmc.psu.edu
Phone: 717-531-0003, ext. 285020

Sanger DNA Sequencing (GENEWIZ service)

Penn State College of Medicine  is partnering with GENEWIZ for Sanger DNA sequencing services.

 GENEWIZ Submission Guidelines

 Ordering Instructions:

1. Register for a GENEWIZ account: https://clims3.genewiz.com/NewAccount.aspx.  When registering for a GENEWIZ account, please enter your lab's specific GENEWIZ Account ID.

2. Once logged into your GENEWIZ account, select "Create a Sequencing Order" from the upper left quadrant of your account home page.

3. Select the sequencing order options that best meet your project
requirements.

4. Enter all order information into the online order form or Excel order form. 

5. Once your Sanger DNA sequencing order is complete, please print the order
receipt, affix labeled samples to order receipt, and place into a Ziploc bag for sample
submission.

6. Place the Ziploc bag containing your order receipt and samples in your GENEWIZ Drop Box at the Penn State College of Medicine, Basic Science Wing, Room C2705 by 4:00 P.M.  (Monday – Friday).

 (Please complete the sample log when dropping off samples at each GENEWIZ Drop Box to ensure effective submission)

7. Sequencing results will be accessible from your GENEWIZ account by 5:00 p.m. the
business day following sample submission.

 Contact GENEWIZ Technical Support
                 dnaseq@genewiz.com
                 908-222-0711 ext. 2
 

Pricing inquiries: please contact Xuan Pan, Manager, Global Business & Account Development xuan.pan@genewiz.com  phone: 908-222-0711 ext. 3555.

For additional questions regarding DNA Sequencing services, please contact Yuka Imamura yimamura@hmc.psu.edu.