The Department of Genetics and Genome Sciences
Genomics Core Sequencing Services:
Frequently Asked Questions (FAQs)
Thanks for your interest in the CWRU Genomics Core and deciding to undertake Next Gen Sequencing! It can
be a daunting task if you are new to Genomics and we are here to help. We ask that you please review our
FAQ to help answer some general questions you may have. After reviewing the FAQ please contact us at
nmb64@case.edu with any further questions or to begin the project planning process.
About the Genomics Core
1. Why should I choose the CWRU Genomics Core?
Experience: The CWRU Genomics Core has been providing quality services for over eight years to the
Case Western Reserve Community, University Hospitals, Cleveland Clinic, the surrounding Cleveland
area, as well as institutions outside of Ohio.
Personalized service: We are happy to help you through every step of your project from consultation on
the proper sequencing technology, sample preparation, through bioinformatics analysis.
Professional Project Management: Your samples, work-order, and time are very important to us.
Better Quality Data: Our unique post-sequencing pipeline offers sophisticated read processing and
contaminant filtering so that you receive only the highest quality data possible.
Premiere Journal Publications: Our clients have published in several high impact journals including
Science, Nature, and Cell.
Discounts: Please contact us to discuss specialized pricing for large volume orders and pilot projects.
2. What services does the Genomics Core have to offer?
The CWRU Genomics Core offers a wide range of services to all investigators at CWRU, its partnering
institutions, as well as external collaborators.
Sequencing: We leverage the Illumina Next Gen Sequencing (NGS) platforms consisting of the
HiScan SQ and Genome Analyzer IIx (GAIIx) instruments. Additionally, we also perform Sanger
sequencing on an Applied Biosystems 3730 DNA Analyzer.
NGS Library Prep: The Genomics Core has hands-on experience with various Illumina NGS DNA
and RNA library prep kits as well as target enrichment technologies for custom capture projects. We
can help you decide which of these kits fits best with your project needs and handle the work for you.
Genotyping/Gene Expression: The Genomics Core provides a variety of Illumina-based
genotyping array options including genome-wide studies with up to 5.0 million markers, customdesigned sets of up to several thousand markers, and small-scale projects comprising only a few
markers. DNA methylation profiling, with single CpG resolution, as well as human and mouse linkage
analysis projects can also be accommodated.
We can also assist with the design of custom genotyping projects.
Next Gen Sequencing Services
3. What types of NGS libraries do you construct?
For DNA libraries we typically use the Illumina library kits, TruSeq and Nextera, for samples including
ChIP-Seq and Whole Genome Sequencing. We also employ the Illumina TruSeq and Epicenter Scriptseq
kits for RNA library construction. We have worked with other library preparation kits including Agilent
and Illumina Custom Capture kits.
4. What are the sample submission requirements for library prep services?


Submit all PURIFIED DNA/RNA samples in 1.5ml tubes, clearly labeled with sample name, the
date, and your name/initials.
Fill out the Library Prep Request form and submit/email any QC performed on the samples.
DNA Libraries
Quantity
Volume
QC required
TruSeq DNA
Nextera DNA
chIP-seq DNA
1ug
50ng
~10ng
< 50ul
< 20ul
< 30ul
260/280: 1.8-2.0
260/280: 1.8-2.0
260/280: 1.8-2.0
0.1-4.0ng
50-250 ng
100-250 ng
< 50ul
< 10ul
< 10ul
RIN: 8.0-10.0
RIN: 8.0-10.0
RIN: 8.0-10.0
3ug
< 100ul
260/280: 1.8-2.0
RNA Libraries
TruSeq RNA
Script Seq – rRNA-depleted
Script-Seq – poly(A) eukaryotic RNA per reaction.
Custom Capture
Agilent Sure Select Target Enrichment
5. How many libraries can I pool/index/plex/barcode in one lane?
For indexing standard DNA and RNA libraries we use the Illumina TruSeq indexing protocol which allows
for a maximum of 24 uniquely indexed sample libraries to be pooled together and sequenced in one
lane. The number of reads needed per sample will dictate how many samples can be pooled per lane.
It is suggested to reduce the number of libraries in a pool when possible to minimize the chances of
uneven sequencing read distribution results. As a general warning read distributions may vary for each
sample in a multi-plexed lane increasing potential variation with each additional sample.
It is possible to pool prokaryotic samples using the Nextera DNA Library Prep kit which has the ability to
pool up to 96 samples. The Nextera kit is a specialized kit and cannot be used for all types of samples
and analysis. If you want to know if your samples fit the kit, contact the Genomics Core for a
consultation.
6. Can I supply my own libraries? What are the requirements?
Yes, the Genomics Core accepts and runs libraries that are not made in our lab. We ask that you
provide any QC (qPCR, Bioanalyzer HS chip, etc) performed on the completed library and fill out the
NGS User Agreement Form. The Genomics Core does offer a library quantification package to check
library quality and will QC all samples that are submitted to determine if they can continue onto
sequencing. When filling out the Agreement form make sure to include all pertinent information,
including samples names, pooling/indexing information and any custom sequencing primers required
for the run.



Submit at least 10ul of DNA/RNA library sample in 1.5ml tube, clearly labeled with sample
name, the date, and your name/initials.
For custom primers, please label the given concentration.
Fill out the Illumina NGS Agreement form and submit/email any QC performed on the libraries.
Please feel free to contact us with questions as you are prepping your samples to ensure that you get
only the highest quality results.
7. How much does it cost?
Please refer to the CWRU Genomics Core pricing list at the end of this document or check out our
website http://genomics.case.edu. We partner with several other cores on campus to provide a full
complement of services to allow investigators to go from tissue to data. One of our partners, the
Translational Research Core, provides DNA/RNA extraction or purification services from all manner of
tissue samples.
Special discounts are available for large scale projects. Please contact Nick Beckloff at
nmb64@case.edu for more information.
8. How much sequencing coverage/sequencing depth/many reads do I need?
The ideal amount of coverage is variable and depends on your specific project. Please read this very
helpful technical note from Illumina on how to best estimate sequencing coverage required for
different types of projects.
www.illumina.com/documents/products/technotes/technote_coverage_calculation.pdf
9. How many reads can I expect per lane on the Illumina HiScan SQ and the GAIIx?
For high quality “Standard DNA” or “Standard RNA” libraries sequenced on our HiScan SQ platform
(using V3 chemistry) we typically estimate reads results of approximately 90M reads (+/- 20%) per lane.
For high quality “Standard DNA” or “Standard RNA” libraries sequenced on our GAIIx platform, we
typically estimate reads results of approximately 35M reads (+/- 20%) per lane.
Please inquire with us to receive our most current sequencing results approximations for specialized
libraries (sRNA, ChIP, RRBS, etc.).
10. What is the average turnaround time?
While we try to process all samples as efficiently as possible the following time frames may vary.
Library Prep: We strive to make libraries within 1-2 weeks upon receipt of samples and reagents. The
total amount of time to process is ultimately dependent on the number, type, and quality of samples.
All samples are QC’ed to ensure quality and if the libraries fail the QC process the PI will be contacted
and we will discuss how to move forward.
Sequencing: We try to obtain a turnaround time of approximately 4-6 weeks (for a full flow cell project
of 7 lanes) upon receipt of samples/libraries passing our quality control testing. This can be extended
by several factors including sample failure, machine down time, or holidays. For expedited service it is
easier for us to run projects that can fill an entire flow cell.
Please note that turnaround times for non-full flow cell projects are completely dependent on other
projects filling the remaining lanes of the flow cell before sequencing can commence.
11. How long will Core hold onto my samples?
The Genomics Core stores all remaining library at -20 degrees for a period of 90 days after full project
completion. Users are welcome to pick up samples at any time before this point.
12. How can I set up a research support contract with the Genomics Core?
Please contact Dr. Nicholas Beckloff (nmb64@case.edu). He will discuss your project with you and
provide you with plans and cost estimates. We can also assist in the preparation of your grants
proposals and manuscripts.
Bioinformatics
13. How will my results be delivered?
Standard Results (base calling, quality scores, FASTQC and FASTQ/BAM files) can be delivered in one of
several ways:




Via a secure FTP site/Helix account
External hard drive
CWRU Galaxy delivery
CWRU High Performance Computing Cluster
CWRU Genomics Core’s unique post-sequencing pipeline offers sophisticated read processing and
contaminant filtering so that you receive only the highest quality data possible.
14. How can I work with the Genomics Core to analyze my sequencing data?
Depending upon your specific needs and in-house resources there are two approaches you may
consider:
1. Typically we QC the data off the sequencer and will do a post-run alignment converting the
data to BAM files. Some labs take their data as FASTQ files and others ask for alignments.
When your needs extend beyond this realm we have the second option available.
2. We collaborate with the Cancer Center Statistics & Bioinformatics Core to provide informatics
and statistics support for all manner of projects.
15. What are the standard bioinformatics options?
Through the activities of our researchers we developed informatics protocols for analyzing sequence
data. At present these include:

Expression Quantitation & Differential Expression Analysis (RNA-Seq)



SNP & Small Indel Prediction
Exome analysis and Variant Detection
De Novo Transcript Assembly of RNA-Seq Data
16. What is your data archiving policy?
The Genetics and Genome Sciences Department has a Data Archival Policy that is required to be signed
before sequencing with the Genomics Core. Once sequencing data has been delivered, the raw images
are discarded and standard output is retained for six months.
Special data storage and delivery requests may be accommodated.
Thank you very much for considering us for your project, if you have any additional questions please email:
nmb64@case.edu. We hope to hear from you soon!
Pricing
Illumina NGS
*Prices include necessary reagents and processing fees; does NOT include library prep fees or QC fees of libraries.
GAIIX
Single Read
36-base run
76-base run
100-base run
HiScan SQ
Price per Lane*
$650
$875
$1,075
Paired-End Read
2x 36-base run
2x 76-base run
2x 100-base run
Single Read
50 base run
$695
100 base run
$925
Paired-End Read
2x 50-base run
$1,500
Price per Lane*
2x 100-base run
$1,200
$1,450
$1,925
$2,385
Informatics
$100/hr
Illumina NGS Library Prep
*Prices include necessary reagents and processing fees; does NOT include sequencing fees or QC fees of libraries
Illumina chIP-seq Sample Prep
Total/sample
Price *
$400
Illumina TruSeq DNA prep
Total/sample
$365
Nextera DNA Prep Kit
Total/1 sample
$280
Total/8 samples
$850
Special Illumina Seq Reagent required for Nextera libraries per flow cell
$90
Illumina TruSeq RNA Prep
Total/1 sample
$370
Script-Seq RNA prep
Total/1 sample
TBD
Total/8 samples
TBD
Exome Capture Library Prep (Agilent)
Total/1 sample
$350
Covaris Shearing and Quality Control (QC) Services
Covaris Shearing
Price *
Total/sample
$10
Qubit of submitted total RNA , DNA, or prepared library
Fewer than 10 samples
n/c
More than 10 samples
$1.00/sample
qPCR of prepared library
Total per sample
$30
Special Illumina Seq Reagent required for Nextera libraries per flow cell
$90
Agilent Bioanalyzer HS Chip of prepared library
Total per chip – 11 samples per chip
$100
Other Services
*For Illumina projects, prices include ONLY processing fee. Reagents are extra and should be purchased directly through Illumina.
Instrument
Applied Biosystems
3730 DNA Analyzer
Price
Sanger Sequencing
$8.00
Per reaction
$6.00
Per reaction per full 96-well plate
EXO/SAP PCR Clean-up
$1.00
Per reaction
Microsatellite/SNPs/SNaPshot
$5.00
Per reaction
$3.00
Per reaction per full 96-well plate
Price *
Instrument
Illumina HiScan &
BeadXpress
Infinium assay
$150
Per 12-sample chip
$200
Per 24-sample chip
GoldenGate assay
$500
Per 96-well plate
VeraCode assay
$500
Per 96-well plate
Gene Expression assay
$150
Per 2 chips (12/24 samples)