About Member of Mid-Atlantic Shared Services Consortium

INACTIVE-SKCCC Microarray Core

The Experimental and Computational Genomics Core (ECGC) at SKCCC now includes new capabilities for Agilent and Illumina EPIC array analysis, Next Generation Sequencing, and Bioinformatics in order to provide integrated services and educational opportunities for the Oncology Center and the broader Johns Hopkins University community.Overview of Services

Overview of Services

Agilent 60-mer oligo arrays with single or dual-color labeling which allows for RNA differential expression, DNA copy number alteration, and gene regulation at promoter regions.
Illumina iScan and BeadChip service provides array tools to detect genome-scale differential DNA methylation and copy number variation (CNV)/single-nucleotide polymorphism (SNP) using genotyping assays.
In-house array printing service offers custom oligonucleotide, PCR fragment, or DNA clone spottingonto glass slides.

Our services include assistance with your experimental design, as well as RNA or DNA isolation from a variety of biological samples.

Leadership

Kornel Schuebel, Ph.D.

Resource Director

kschueb1@jhmi.edu

410-614-0445

Leslie Cope, Ph.D.

Computational Biology and Biostatistics

lcope1@jhmi.edu

Jennifer Meyers

Senior Lab Manager

Jmeyers6@jhmi.edu

Hai Xu

Specialist/Senior Technician

hxu1@jhmi.edu

Liping Suo

Lab Technician

lsuo1@jhmi.edu

Location and hours of operation

Hours

Location

9 am - 5pm

Monday - Friday

ECGC

CRB2, 113

Map

Contacts

Name	Role	Phone	Email	Location
Kornel Scheubel, PhD	Resource Director	410-614-0445	kschueb1@jhmi.edu

Price List

Name	Description	Price
4x 44K Expression array, Process Only		Inquire
Agilent (species other than human) 4x 44K Expression array	One sample for each array. Service recommends to include technical duplicates in the assay. Sample Requirements: 1.0 ug RNA with concentration of 50 ng/ul or higher. Minimum sample number: 4	Inquire
Agilent (species other than human) 4x 44K Expression array, low input	One sample for each array. Service recommends to include technical duplicates in the assay. Sample Requirements: 50 - 200 ng RNA input with concentration of 25 ng/ul or higher. Minimum sample number: 4	Inquire
Agilent Human v2, 4x 44K Expression array	One sample for each array. Service recommends to include technical duplicates in the assay. Sample Requirements: 1.0 ug RNA with concentration of 50 ng/ul or higher. Minimum sample number: 4	Inquire
Agilent Human v2, 4x 44K Expression array, low input	One sample for each array. Service recommends to include technical duplicates in the assay. Sample Requirements: 50 - 200 ng RNA with concentration of 25 ng/ul or higher. Minimum sample number: 4	Inquire
Array Data Analysis Software Training	Consult with Core	Inquire
Basic Array Data Analysis/Bioinformatics	Consult with Core	Inquire
DNA Isolation	DNA isolation from cultured cells or frozen tissue. Sample Requirements: Minimum cell number: 5x 10⁵. Minimum tissue weight: 10 mg. Minimum sample number: depend on array type to be used	Inquire
DNA PicoGreen Assay for Quantification		Inquire
DNA quality check using PicoGreen/TapeStation	Require minimum sample number: 8	Inquire
DNA TapeStation analysis	Require minimum DNA concentrations to be 10 ng/ul measured by PicoGreen kit. Minimum sample number: 8	Inquire
Illumina Methylation EPIC BeadChip for FFPE samples including DNA restore.	Service requires at least 500 ng DNA to be submitted with concentration of 10-100 ng/ul measured using Qubit. Service includes bisulfite conversion.	Inquire
Illumina Methylation EPIC BeadChip, 8 or in multiple of 8 samples	Service requires at least 250 ng DNA to be submitted with concentration of 10-100 ng/ul measured using Qubit. Samples should be submitted in 96-well microplate. Service includes bisulfite conversion.	Inquire
Illumina Methylation EPIC BeadChip, Process Only	User purchases and provides arrays. Service includes bisulfite conversion.	Inquire
Illumina SNP array service	Customers who need this service can contact core's manager for suitable array to be used and get cost estimate.	Inquire
qPCR target validation using TaqMan PCR array plates	Consult with Core Manager	Inquire
RNA Bioanalyzer Analysis	RNA quality accessment but not for array Sample Requirements: 5 ul RNA with concentration of 20 ng/ul or higher. Minimum sample number: 11	Inquire
RNA Isolation	RNA isolation from cultured cells or frozen tissue. Sample Requirements: Minimum cell number: 5x 10⁵. Minimum tissue weight: 10 mg. Minimum sample number: depend on array type to be used	Inquire
RNA quality check using Nanodrop/Bioanalyzer	Require minimum sample number: 10 (Pico kit) or 11 (Nano kit)	Inquire
SurePrint G3 Human or Mouse Array CGH 4X180K, Process Array only	One sample plus a reference for each array; User provides array Sample Requirements: 1.0 ug RNA with concentration of 50 ng/ul or higher. Minimum sample number: 4 with reference	Inquire
SurePrint G3 Human or Mouse Array CGH, 4x180K	One sample plus a reference for each array Sample Requirements: 1 – 3 ug genomic DNA. Minimum sample number: 4 with reference	Inquire
Total RNA/microRNA isolation from FFPE sections	Total RNA including microRNA isolation from FFPE sections using Qiagen FFPE miRNesy kit with small RNA quality check using Bioanalyzer. Apply for array or Nanostring assay. Sample Requirements: Minimum section number: 5. Minimum section thickness 10 um. Minimum sample number: 8 or 12	Inquire

Search available services: View: by category alphabetically

Name	Description	Price
▼ ► CGH Array (2)
SurePrint G3 Human or Mouse Array CGH 4X180K, Process Array only	One sample plus a reference for each array; User provides array Sample Requirements: 1.0 ug RNA with concentration of 50 ng/ul or higher. Minimum sample number: 4 with reference	Inquire
SurePrint G3 Human or Mouse Array CGH, 4x180K	One sample plus a reference for each array Sample Requirements: 1 – 3 ug genomic DNA. Minimum sample number: 4 with reference	Inquire
▼ ► DNA-Methylation (3)
Name	Description	Price
Illumina Methylation EPIC BeadChip for FFPE samples including DNA restore.	Service requires at least 500 ng DNA to be submitted with concentration of 10-100 ng/ul measured using Qubit. Service includes bisulfite conversion.	Inquire
Illumina Methylation EPIC BeadChip, 8 or in multiple of 8 samples	Service requires at least 250 ng DNA to be submitted with concentration of 10-100 ng/ul measured using Qubit. Samples should be submitted in 96-well microplate. Service includes bisulfite conversion.	Inquire
Illumina Methylation EPIC BeadChip, Process Only	User purchases and provides arrays. Service includes bisulfite conversion.	Inquire
▼ ► Data Analysis (1)
Name	Description	Price
Basic Array Data Analysis/Bioinformatics	Consult with Core	Inquire
▼ ► Expression Array (5)
Name	Description	Price
4x 44K Expression array, Process Only		Inquire
Agilent (species other than human) 4x 44K Expression array	One sample for each array. Service recommends to include technical duplicates in the assay. Sample Requirements: 1.0 ug RNA with concentration of 50 ng/ul or higher. Minimum sample number: 4	Inquire
Agilent (species other than human) 4x 44K Expression array, low input	One sample for each array. Service recommends to include technical duplicates in the assay. Sample Requirements: 50 - 200 ng RNA input with concentration of 25 ng/ul or higher. Minimum sample number: 4	Inquire
Agilent Human v2, 4x 44K Expression array	One sample for each array. Service recommends to include technical duplicates in the assay. Sample Requirements: 1.0 ug RNA with concentration of 50 ng/ul or higher. Minimum sample number: 4	Inquire
Agilent Human v2, 4x 44K Expression array, low input	One sample for each array. Service recommends to include technical duplicates in the assay. Sample Requirements: 50 - 200 ng RNA with concentration of 25 ng/ul or higher. Minimum sample number: 4	Inquire
▼ ► SNP/CNV (1)
Name	Description	Price
Illumina SNP array service	Customers who need this service can contact core's manager for suitable array to be used and get cost estimate.	Inquire
▼ ► Sample Isolation/Preparation/Quality Check (8)
Name	Description	Price
DNA Isolation	DNA isolation from cultured cells or frozen tissue. Sample Requirements: Minimum cell number: 5x 10⁵. Minimum tissue weight: 10 mg. Minimum sample number: depend on array type to be used	Inquire
DNA PicoGreen Assay for Quantification		Inquire
DNA quality check using PicoGreen/TapeStation	Require minimum sample number: 8	Inquire
DNA TapeStation analysis	Require minimum DNA concentrations to be 10 ng/ul measured by PicoGreen kit. Minimum sample number: 8	Inquire
RNA Bioanalyzer Analysis	RNA quality accessment but not for array Sample Requirements: 5 ul RNA with concentration of 20 ng/ul or higher. Minimum sample number: 11	Inquire
RNA Isolation	RNA isolation from cultured cells or frozen tissue. Sample Requirements: Minimum cell number: 5x 10⁵. Minimum tissue weight: 10 mg. Minimum sample number: depend on array type to be used	Inquire
RNA quality check using Nanodrop/Bioanalyzer	Require minimum sample number: 10 (Pico kit) or 11 (Nano kit)	Inquire
Total RNA/microRNA isolation from FFPE sections	Total RNA including microRNA isolation from FFPE sections using Qiagen FFPE miRNesy kit with small RNA quality check using Bioanalyzer. Apply for array or Nanostring assay. Sample Requirements: Minimum section number: 5. Minimum section thickness 10 um. Minimum sample number: 8 or 12	Inquire
▼ ► Training/Instruction (1)
Name	Description	Price
Array Data Analysis Software Training	Consult with Core	Inquire
▼ ► qPCR validation (1)
Name	Description	Price
qPCR target validation using TaqMan PCR array plates	Consult with Core Manager	Inquire