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 staffs are available for assisting project operation. 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 to the prior consultation and agreement on the design of experiment. We develop new applications to accommodate state-of-the-art NGS technologies. We conduct sequencing reads alignment, secondary analysis (quantitation, variant calling, functional annotation, visualization, etc) and follow-up the interpretation of the results. We support grant writings and educate/train students/post-docs for hands-on NGS processing.
Please contact Director (Yuka Imamura, x289250) for more information (http://sites.psu.edu/yuka/).
- NextGen Sequencing
- Custom DNA Sequencing
- Sample QC/QA
- QIA symphony DNA/RNA extraction robot
- Bullet Blender (high throughput tissue homogenizer)
- Covaris adaptive focused acoustics ultrasonicator E-series
Sample quantitation and quality control
- Agilent 2100 Bioanalyzer
- Nanodrop ND-1000 spectrophotometer
- Qubit fluorometer
- Molecular Devices UV/Vis/Fluor Spectrophotometer available in Drug Discovery Core
- ABI QuantStudio 12K Flex system with available OpenArray block
- ABI QuantStudio 3D digital PCR system
Next Generation Sequencing (NGS)
- ABI 3130XL Capillary sequencer (Sanger sequencing and associated genotyping or DNA fingerprinting applications)
- Agilent Genespring
- Illumina GenomeStudio
- Illumina iCompute
- Ingenuity Pathway Analysis: Please contact Research Computing for information on IPA and Genespring
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.
FEES per sample:
|200 ul Whole Blood DNA prep||$ 5.90|
|400 ul Whole Blood DNA prep||$ 7.40|
|1000 ul Whole Blood DNA prep||$ 10.80|
|200 ul DNA prep buffy coat||$ 5.90|
|400 ul DNA prep buffy coat||$ 7.40|
|400 ul RNA prep||$ 6.40|
|800 ul RNA prep||$ 12.00|
|1000 ul Saliva DNA prep||$ 10.80|
For more information, contact Sue Patrick x5676 firstname.lastname@example.org
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. Fees: $8.00/per sample (includes specialty tube). Please contact Sue Patrick x5676 email@example.com for more details.
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 for more information.
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||service type||cost per sample*|
|whole genome sequencing||WGS library prep||$50.12|
|whole exome sequencing||(Human) (minimum input DNA 1 ng for intact DNA, under R&D for FFPE DNA)||$362.18|
|exome (other species, mouse, bovine, zebrafish)||please inquire|
|ChIP sequencing||ChIP-seq library prep (minimum input DNA 0.5 ng)||$50.12|
|Low input ChIP-seq library prep (minimum input DNA 0.05 ng)||$115.33|
|Methylation sequencing||ERRBS (enhanced reduced representation of bisulfite sequencing) library prep||$99.33|
|RNA sequencing||PolyA RNA seq library prep (strand-specific, minimum input RNA 50 ng)||$69.01|
|Total RNA seq library prep (rRNA depleted, human, mouse, rat, standard rRNA-depletion, strand-specific, minimum input RNA 100 ng)||$160.55|
|Low Input RNA-seq library prep (minimum input RNA 10 pg, or single cell)||$80.88|
|Low Input cDNA synthesis (minimum input RNA 10 pg, or single cell)||$70.35|
|Degraded Low Input RNA-seq library prep (minimum input RNA 10 ng)||$194.58|
|Degraded Low Input cDNA synthesis||$144.46|
|Small RNA seq library prep (minimum input RNA 1 ug)||$96.96|
|Low input small RNA-seq library prep (minimum input RNA 100 ng)||$114.97|
|Single cel RNA-seq (up to 96 samples)||please inquire|
*QC bioanalyzer run will be added (usually 3 runs ($180) up to 11 samples)
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 MGCF also provides genotyping, SNPlex analysis and fragment analysis.
- Custom Sequencing - $6.50 per template sequenced
- BAC samples - $9.50 per sequence
- Fragment analysis - $2.00 per sample.
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 location \\hersheymed.net\files\research\corefacility\Results\DNA-Sanger Sequencing.
Please save completed Submission forms in the same network folder.
You may also submit via Geneus LIMS LabLink
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 reaction. For 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. - see full list of available primers.
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 eg. DMSO to minimize 2° structure in GC rich templates, 3) indicate if the DNA template is anything other than plasmid DNA, eg. 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)
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.
- The cost for RNA QC is $60 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).
Acknowledgement and thanks for the Bioanalyzer images used
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
If you can not Print as a pdf, then 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.
HCAR researchers may place their samples in the box located in the Freeman lab, room 3200.
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
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 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.
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.
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.
Gene Expression Microarrays
The Genome Sciences Core uses the Illumina platform which comes in several formats
· Mouse Whole Genome Array (multiple of 6) - $345/array
· Mouse RefSeq8 Array (multiples of 8, only sequences are RefSeq ) - $250/array.
· Human HT_12 arrays (multiples of 12 ) - $220/array.
· For focused genotyping/CNV studies the VeraCode platform using the BeadXpress instrument is extremely powerful. This platforms lets investigators choose their specific SNPs of interest in 48-, 96-, 144-, 192-, or 384-plex formats. Contact the Core for more information.
For experimental scheduling and Core closures please see:
The Genome Sciences Core is located in C2705.
Director: Yuka Imamura Kawasawa, Ph.D
Phone: 717-531-0003 x289250
Sanger DNA Sequencing (GENEWIZ service)
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
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
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 5:00 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.
For additional questions regarding DNA Sequencing services, please contact Yuka Imamura firstname.lastname@example.org.