Integrated Genomics Core

The Integrated Genomics Core, operational since October 2008, provides Microarray technology, Pyrosequencing, and Next Generation Sequencing to researchers at GHSU and collaborating institutions.

Contact: Dr. Sam Chang, Research Manager. (P) 706-721-5471. CHCHang@georgiahealth.edu
             Dr. Eiko Kitamura, (P) 706-721-5471. EKitamura@georgiahealth.edu

Oversight Committee: 
--Sequencing & Microarray--
Sam Chang 
Eiko Kitamura
Lesleyann Hawthorn
John Cowell
Phillip Buckhaults
Huidong Shi
Keith Robertson 

 

** Please note that pricing is subject to the changes of suppliers.

Next Generation Sequencing

***The Pricing Lists of new Hi-Seq V3 version have been added and updated.

** If you have used our service in the past, please take the time to fill out this survey:
   http://www.zoomerang.com/Survey/WEB22EKJWPVXK4

With the addition of the Illumina GAIIx and HiSeq 2000 system, the Core also offers single read, paired-end, and multiplex sequencing. The Core also offers library preparation services for DNA-seq, RNA-seq, and other standard sequencing libraries. Each flow-cell contains 8-lanes, and each lane can process up to 3 GB of sequence for GAIIx and 12 GB of sequence for HiSeq 2000 V2, further, nearly 20-25 GB of sequence for new Hi-Seq 2000 V3. 

Equipment / Infrastructure

• Agilent ^® 2100 Bioanalyzer
• NanoDrop 1000
• QuBit Fluorometer
• Illumina Genome Analyzer IIx
• Illumina HiSeq 2000 V2 & V3
• cBot Cluster Generation System
• qPCR (ABI)
• Pyrosequencers (Biotage;PyroMark MD

Applications

• DNA Sequencing
• Gene Regulation Analysis
• Sequencing-Based Transcriptome Analysis
• SNP Discovery and Structural Variation Analysis
• Cytogenetic Analysis
• DNA-Protein Interaction Analysis (ChIP-Seq)
• Sequencing-Based Methylation Analysis

Data Analysis **

• CASAVA (Eland Alignment & SNP calling)
• Partek Genomics Suite
• CLC Bio
• TrueSeqEnrichment Analysis Tool
• BWA Alignment
• GATK1.5 (SNP135)
• Annovar
• GSNAP & GMAP
• Seqgene
• ExomeCNV
• Tophat Fusion
• Tools for DNA-Seq, RNA-Seq and Chip-Seq analyses.
• IPA Pathway Analysis

**Initial data analysis in FASTQ format included in sequencing fee**

• The CASAVA1.8 based BAM file including realign.bam is $80/sample, an entire Standard sequencing analysis would be $120/sample, and IPA pathway analysis will be $20/sample plus.

 

Library Preparation/Quality Assessment: 

DNA-Seq  (Genomic Library)	Library Preparation	$250.00/sample
mRNA-Seq	Library Preparation	$250.00/sample
DNA Exome Capture Sample Prep (plus Agilent SureSelect Kit)	Library Preparation	$650.00 /sample
Chip-Seq (> 10 ng Enriched DNA with INDEX)	Library Preparation	$250/sample
*We will not guarantee number of reads or number of captured regions if the libraries are prepared by the individual investigators. We can only guarantee the performance of libraries prepared by sequencing facility personnel.
Illumina GAIIx Sequencer Pricing List
36-cycle  Single-end Read		$850.00/lane
72-cycle Single-end Read		$1150.00 /lane
36-cycle Paired-end Read		$1400.00/lane
72-cycle Paired-end Read		$2000.00 /lane

* All off-campus sequencing runs will be an additional 30% charge.

 Library Preparation/Quality & Quantity Assessment: 

 

DNA-1000 Chip	Quality Assessment:          $45.00/sample
RNA-Nano Chip	Quality Assessment:          $45.00/sample
DNA Hi-sensitive Chip	Quality Assessment:          $45.00/sample
Qubit Measurement (>1 ng/ul) Quantity Assessment:	Quality Assessment:          $2.50/sample
qPCR Reaction	Quality Assessment:          $100/7 lanes
*Particularly for the Hi-sensitive DNA Chip users, please come up with the concentrations preferably measured by qubit, that by NanoDrop are also acceptable.  * The fee for users using qPCR machine on their own will be $25/run.

Illumina HiSeq V2 Sequencer Pricing List

50-cycle Single-end Read	$900.00/lane
100-cycle Single-end Read	$1300.00/lane
200-cycle Single-end Read	$2000.00/lane

 

50-cycle Paired-end Read	$1500.00/lane
100-cycle Paired-end Read	$2200.00/lane

 

Illumina HiSeq V3 Sequencer Pricing List

50-cycle Single-end Read	$1100.00/lane
100-cycle Single-end Read	$1600.00/lane
200-cycle Single-end Read	$2250.00/lane
50-cycle Paired-end Read	$1900.00/lane
100-cycle Paired-end Read	$2500.00/lane

 

* All off-campus sequencing runs will be an additional 30% charge.

Sequencer Request Form
Please fill out the detailed information regarding the prepared libraries based on the Illumina guideline.

Download the Sequencer Request Form

 

Microarray Technology

**If you have used our service in the past, please take the time to fill out this survey:
   http://www.zoomerang.com/Survey/WEB22EKP5JYHVP

Microarrays are performed through Affymetrix ^® and Agilent ^®  Scanner Platforms. The combination of the two platforms allows for nearly an unlimited use of different array formats from a multitude of different suppliers.

Arrays: exon-specific, oligonnucleotide and genome-wide
The gene expression arrays that provide estimates of mRNA levels in tumors have given rise to exon-specific arrays that can identify both gene expression levels, alternative splicing events and mRNA and miRNA processing alterations. Oligonucleotide arrays are also being used to interrogate single nucleotide polymorphisms (SNPs) throughout the genome for linkage and association studies, and these have been adapted to quantify copy number abnormalities and loss of heterozygosity events.

Genome-wide tiling arrays have been developed to identify as yet unknown transcripts. Global DNA methylation changes can be detected using array platforms. High-resolution copy-number and LOH for Human and Mouse can also be performed, as well as genome-wide association studies. Additionally, it has now become possible to identify DNA-protein interactions using chromatin immunoprecipitation (ChIP) on Chip protocols. With all of these capabilities becoming routine in genomics laboratories, the idea of a systematic characterization of the sum genetic events that give rise to a cancer cell is rapidly becoming a reality.

Equipment / Infrastructure

• Affymetrix ^® GeneChip Scanner 3000 7G Plus
• Affymetrix ^® Hybridization Oven 640
• Affymetrix ^® Fluidics Station 450 (x2)
• Agilent ^® Microarray Scanner
• Agilent ^® Hybridization Oven for Array Slides
• Agilent ^® 2100 Bioanalyzer
• Applied Biosystems GeneAmp 9700 Thermocycler
• NanoDrop 1000

Data Analysis *

• Affymetrix ^® Genotyping Console
• Affymetrix ^® Expression Console
• Agilent ^® GeneSpringGX
• Agilent ^® Feature Extraction
• Ingenuity Pathway Analysis
• Partek Genomics Suite
• Gene Set Enrichment Analysis (GSEA)
• BioConductor

Bioinformatics and support

The Core aims to provide Cancer Center researchers access to microarray technology and bioinformatics at an affordable cost.* It offers consultation, training and educational seminars on:

• analysis of microarray data
• programs designed to analyze large data sets
• gene expression
• the roles of DNA sequence variation in the genome

Software, training and support is also available for researchers to enable them to analyze large data sets and obtain meaningful results from these experiments. A large number of state-of-the-art programs are available to afford analyses of different data types and the expertise is available to implement and advise on their usage.

*Initial data analysis included in array fee*

BioAnalyer	Platform	Cancer Center Member	Off Campus
RNA 6000 Nano	Agilent	$45.00	$75.00
RNA 6000 Pico	Agilent	$45.00	$75.00
Small RNA	Agilent	$55.00	$75.00
DNA 1000	Agilent	$45.00	$75.00
DNA 7500	Agilent	$45.00	$75.00
DNA 12000   DNA Hi-Sensitivity	Agilent   Agilent	$45.00   $45.00	$75.00   $75.00

 

Human Test	Platform	Cancer Center Member	Off Campus
Expression
miRNA Microarray	Agilent	$400.00	$500.00
Gene 1.0 ST Whole Transcript	Affymetrix	$400.00	$550.00
Exon 1.0 ST Whole Transcript	Affymetrix	$700.00	$800.00
U133 Plus 2.0 Expression	Affymetrix	$675.00	$750.00
miRNA Microarray	Affymetrix	$350.00	$450.00
CGH/SNP
SNP 6.0	Affymetrix	$600.00	$800.00
SNP 5.0	Affymetrix	$500.00	$650.00
250K	Affymetrix	$400.00	$550.00
FFPE 250K	Affymetrix	$450.00	$650.00
CpG Island 1x244	Agilent	$840.00	$940.00

 

Mouse Test	Platform	Cancer Center Member	Off Campus
Expression
Gene 1.0 ST Whole Transcript	Affymetrix	$400.00	$500.00
Exon 1.0 ST Whole Transcript	Affymetrix	$700.00	$850.00
Mouse 430 2.0	Affymetrix	$675.00	$850.00
CGH/SNP
244K CGH	Agilent	$800.00	$975.00
105K CGH	Agilent	$500.00	$650.00
44K CGH	Agilent	$375.00	$500.00
CpG Island 2x105K	Agilent	$800.00	$975.00

 

Rat Test	Platform	Cancer Center Member	Off Campus
Expression
Gene 1.0 ST Whole Transcript	Affymetrix	$400.00	$500.00
Exon 1.0 ST Whole Transcript	Affymetrix	$700.00	$800.00
Rat Genome 230 2.0	Affymetrix	Inquire	Inquire
CGH
244K	Agilent	Inquire	Inquire
105K	Agilent	Inquire	Inquire

 

Other Species	Platform	Cancer Center Member	Off Campus
Expression
Zebrafish Genome Array	Affymetrix	$550.00	$650.00
Other Species	Affymetrix and Agilent	Inquire	Inquire
Yeast Genome 2.0 Array	Affymetrix	$400.00

*Inquire for unlisted array availability*
 

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