Facility details and available services

Genome Sciences Core Facility

Facility Details: (last updated 4/29/15)

Nucleic acid processing and analysis: The Facility maintains equipment for nucleic acid extraction (QIAsymphony and Bullet Blender), sonication (Covaris adaptive focused acoustics ultrasonicator E-series), quantitation and quality control (Agilent 2100 Bioanalyzer, Nanodrop Spectrophotometer, Qubit, and access to a Molecular Devices FlexStation 3 UV/Vis/Fluor spectrophotometer). An LifeTech QuantStudio 12K Flex system with robotic plate handler and QuantStudio 3D digital PCR system is available for qPCR gene expression and genotyping services. The Facility provides custom Sanger sequencing of plasmid, PCR and BAC templates. We can also run fragment analysis assays including footprinting, microsatellite, loss of heterozygosity (LOH), SSCP, RFLP and genotyping/SNPlex (multiplexed SNP analysis). Cost for each service is as follows (we allow walk-up and free usage of Nanodrop and Qubit, please inquire for the usage of FlexStation 3) :

Sample prep and PCR service for base cost -1 sample cost per additional sample
RNA isolation $14.5
DNA isolation $8.7
Covaris $8.00
Bioanalyzer (DNA, RNA, protein) (up to 11-12 samples) $60
cDNA synthesis $1.87
Usage of QuantStudio 12K Flex $14.00
Kapa library qPCR $33.19 $1.52
Digital qPCR $10.50
GoTaq PCR $2.16
QIAsymphony service cost per sample
Whole Blood DNA prep 200 $5.90
Whole Blood DNA prep 400 $7.40
Whole Blood DNA prep 1000 $10.80
DNA prep buffy coat 200 $5.90
DNA prep buffy coat 400 $7.40
RNA prep 400 $6.40
RNA prep 800 $12.00
PAXgene_RNA $12.00
Saliva DNA prep 1000 $10.80

 

Sanger sequencing cost per sample
Custom Sequencing $6.50
BAC samples $9.50
Fragment analysis $2.00

 

Microarray: The Facility offers Illumina platforms as the main microarray-based procedure for genotyping and gene expression. The recently acquired iScan system allows high-throughput and cost-effective microarray analysis of genotyping, gene expression, copy number analysis, methylation analysis and LOH studies. Roche and Agilent microarray equipment is also available. Individual SNP calls can be confirmed by PCR tools described above. Listed below are the costs of some popular microarrays.

Microarray service minimum sample number required cost per sample
Infinium Omni 2.5 (16 samples) 16 214.13
Infinium Omni 2.5 (48 samples) 48 200.63
Human Omni 5 16 319.17
Human Omni Express-24 v1.0 48 149.65
Infinium Methylation 48 334.99
Human gene expression 24 98.72
Mouse gene expression 24 132.65

 

Next Generation Sequencing platforms: For next generation sequencing projects the Facility offers a range of workflows depending on investigator needs and number of reads/length of sequence required for the project. The Facility contains a MiSeq system to perform low output applications (from 300 Mb to 7.5 Gb in ~4 to 39 hours) and a HiSeq 2500 system, which allows data collection in both rapid run (up to 90 Gb/flow cell, 2×150 bp, in 40 hours) and high output modes (up to 300 Gb/flow cell, 2×100 bp, in ~11 days) on either one or two flow cells. The Facility also maintains a LifeTech Ion Proton DNA sequencer for targeted sequencing and exome sequencing (10 Gb with sequencing run time of 2-4 hours). An Apollo 324 robotic system supports a variety of automated library preparation protocols for whole genome, whole exome, ChIP-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.

Penn State Hershey Genome Sciences Facility sercive pricing (as of Apr 2015)
service pre-service QC (separate charging) workflow price estimation
WGS QC gDNA (Qubit, OD, agarose gel run): ask customers to run We will outsource mammalian WGS projects $1,500
Exome QC gDNA (Qubit, OD, agarose gel run): ask customers to run Agilent Exome 75Mb postcapture seq at X50 (10 samples per 2 rapid lanes), more as needed $771
Agilent Exome 51Mb precapture seq at X50 (15 samples per 2 rapid lanes), more as needed $609
Nimblegen please inquire
IDT please inquire
various targeted panels please inquire
mRNA-seq QC total RNA (OD, BioA): ask customers to run 1. Stranded poly-A selected single end seq at 25M reads of 1X50 (default), more as needed $227
2. Straned poly-A selected paired end seq at 25M reads of 2X50 (default), more as needed $391
3. Stranded total (rRNA reduced) single end seq at 25M reads of 1X50 (default), more as needed $282
4. Stranded total (rRNA reduced) paired end seq at 25M reads of 2X50 (default), more as needed $482
5. Low Input RNA-seq library prep (minimum input RNA 10 pg, or single cell) seq at 10M reads of 1X50 (default), more as needed $151
6. Degraded Low Input RNA-seq library prep (minimum input RNA 10 ng) seq at 10M reads of 1X50 (default), more as needed $265
Single cell mRNA-seq hand-picked single cell to be lysed/snap-frozen (no QC required) single cell mRNA-seq (per 1 sample) seq at 10M reads of 1X50 (default), more as needed $151
Cell number and size distribution cDNA synthesis (up to 96 single cells, automated) $1,500
library prep and sequencing 1 Output lanes at 1X50 (48-96 single cells) seq at 5M reads of 1X50 (default), more as needed $1,264
small RNA-seq QC total RNA (OD, BioA): ask customers to run Small RNA seq library prep (minimum input RNA 1 ug) seq at 5M reads of 1X50 (default), more as needed $146
Low input small RNA-seq library prep (minimum input RNA 100 ng) $164
ChIP-seq QC input DNA (Qubit, OD, BioA): ask customers to run ChIP-seq library prep (minimum input DNA 0.5 ng) seq at 15M reads of 1X50 (for TF) $150
seq at 30M reads of 1X50 (for histone marks) $208
Low input ChIP-seq library prep (minimum input DNA 0.05 ng) seq at 15M reads of 1X50 (for TF) $172
seq at 30M reads of 1X50 (for histone marks) $231
Methyl-seq (ERRBS) QC input DNA (Qubit, OD): ask customers to run ERRBS seq at 35M reads of 1X50 $335

 

Seq only 2X: paired end, 1X: single end
HiSeq 2500
Rapid per 2 lanes (need 2 lanes to run the flow cell) Reagent kit No. of reads (million) per flow cell (2 lanes run mixed/run together) cost 
2X100 300 $3,823.32
2X50 300 $3,714.45
1X100 300 $2,406.68
1X50 300 $1,756.73
Rapid per lane (need 2 lanes to run the flow cell, cBot duo to separate lane 1 and 2) Reagent kit No. of reads per lane cost 
2X100 150 $2,129.66
2X50 150 $2,075.23
1X100 150 $1,421.34
1X50 150 $1,096.37
Output per lane (need 8 lanes to run the flow cell) Reagent kit No. of reads per lane cost
2X100 175 $2,145.10
2X50 175 $1,612.11
1X100 175 $1,284.72
1X50 175 $876.62
MiSeq
versions MiSeq reagent kit No. of reads (million) cost
v2 series 2X250 15 $1,271.10
2X150 15 $1,164.39
2X50 15 $955.93
2X150 micro (small genome) 4 $1,006.31
2X150 nano (small genome, QC) 1 $746.39
v3 series 2X75 25 $1,209.63
2X300 25 $1,820.22

 

Bioinformatics Support: The Penn State College of Medicine has three dedicated High Performance Computing (HPC) systems with a total of 136 CPU Cores, 768GB RAM and 50TB of local storage in addition to the 80 TB Storage Area Network (SAN). For the non-human subject samples, we also have access to the world class High Performance Compute systems at Penn State University Park, including BioSTAR (512 processor cores, 4 TB of aggregate memory, and 624 TB of disk storage) and CyberSTAR (1,920 cores and 7.68 TB memory, and 650 TB storage). We conduct sequencing reads alignment, secondary analysis (quantitation, variant calling, functional annotation, visualization, etc), as well as statistical analysis correlating genomic with phenotypic information. There is no charge for the consultation and we encourage each investigator to make an appointment with Director/staff in advance to secure enough time for discussion. Director’s availability is found in the 5th tab of below web site(http://sites.psu.edu/yuka/). Bioinfomatics service will be charged at $50 per hands on hour. Each project is different, so investigators are encouraged to contact us to estimate the necessary hours for each project.

Bioinformatics support cost per hour
Bioinformatics support $50.00