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The Experimental and Computational Genomics Core (ECGC) integrates all the Cancer Genomics services in the SKCCC next generation sequencing, microarrays, bioinformatics, and genomics education. The primary mission of the shared resource is to allow investigators to harness the ongoing revolution in cancer genomics to accelerate their basic discovery and translational research.

Start a Project with ECGC and Request a Consult

The ECGC holds consultation meetings every Friday from 10AM to Noon via Zoom. These meetings are by appointment only. If you would like to initiate a project, and to schedule a consultation meeting, please schedule a consult meeting using the link below.

Areas of Expertise:

Gene Expression Analysis, Proteomics, Microarray Design, Gene Function Analysis, Cancer Risk Prediction, Gene Regulation, Sequence Alignment, Modeling of Signaling Pathways, Transposon Biology 

Other Interactions:

Microarray Core, Mass Spectrometry Core, and Research Information Technology Shared Resource, SPORES, program project grants.

Services Provided:

  • Assist with data acquisition, including study design, access to public data sources and genomic annotation databases and data storage.
  • Statistical quality control for data from high throughput genomic technologies, including data preprocessing, and artifact discovery.
  • Data analysis, including visualization and biostatistical modeling.
  • Assist with grant and manuscript preparation, and software development.
  • Technical support for bioinformatic software, databases and technologies.
  • Development of innovative bioinformatic methodologies and tools.
  • Mentor faculty, fellows and students with interest in bioinformatics research.

Bioinformatics

Dr. Leslie Cope leads the shared resource in methods development and analyses of high-throughput cancer datasets, including computational methods to handle molecular profiling, spatial molecular and imaging technologies.  

The goal of the Bioinformatics consulting service is to help investigators that use genomic technologies to identify study designs, database solutions, data analysis strategies, and appropriate bioinformatics collaborations for their projects. 

ECGC Directors

Image of Leslie Cope

Leslie Cope, Ph.D

Associate Professor of Oncology

JHU Faculty Profile

Pricing

Package Pricing

 Library Kit & Platform DesignOutput / CoveragePrice per sample
WGSKit: TruSeq Nano DNA Library kit Platform
NovaSeq6000 S4 (150bp PE)
mappable mean depth 15X$580
  mappable mean depth 30X$1,019
  mappable mean depth 60X$1,981
  mappable mean depth 90X$2,918
  raw data 100Gb$902
WESKit: Agilent SureSelect V5 Platform
NovaSeq6000 S4 (150bp PE)
100X raw depth coverage$243
  200X raw depth coverage$338
  400X raw depth coverage$465
  600X raw depth coverage$620
Bulk RNAseqKit: TruSeq Stranded Total RNA Library kit Platform
NovaSeq6000 S4 (150bp PE)
60M total reads
(30M read1 and read2)
$374
  50M total reads
(25M read1 and read2)
$355
  100M total reads
(50M read1 and read2)
$450
 Expedited Services available for some Please inquire

10X Genomics Single Cell RNAseq

 # of samplesPrice per sample
10X 3′ Digital Gene Expression (DGE)1-16 samples$1,906
10X 3′ Digital Gene Expression (DGE)> 16 samples$2,060
10X 5′ Digital Gene Expression (DGE)1-16 samples$1,906
10X 5′ Digital Gene Expression (DGE)> 16 samples$2,060
   
Additions:  
10X 5′ DGE with VDJ (TCR or BCR profiling)1-16 samples$361
10X 5′ DGE with VDJ (TCR or BCR profiling)> 16 samples$464

Microarray Services

Service TypeService Name (as listed in iLab)Array Purchase Cost Per Sample
Illumina Methylation 850 (standard)Illumina EPIC human
methylation 750, FFPE
$361
Illumina Methylation 850
(Low Input)
 $567
Illumina Methylation 850 FFPEIllumina EPIC human
methylation 750, FFPE
$361
Illumina MethylationMouse EPIC array multiple of 12$340
Genome Restoration $155

Bioinformatics Services

 Project executionUnit priceCharge for large sample size
RNASeq, ChipSeq, Exome, ATACSeq, Amplicon,
MicroRNA, VDJ, DGE, Visium and Long Ranger
$618$93/sample$155/additional 30 samples
Whole Genome Sequencing$618$186/sample$155/additional 30 samples
Multiome$927$186/sample$155/additional 30 samples
HTO/CSP and MULTISeq$1,854$93/library 
Data Delivery via One Drive $73 
Data Delivery via hard drive $186
per 2TB drive
 
Collaborative Service Package 5% FTE / $6,180 

Full Pricing List of Wet Lab Services

Service Unit Price Unit
ECGC Lab processing fee $62 sample
ECGC Lab processing fee custom projects $103 sample
Expedited Service available Contact Us sample
RNA Isolation (cell pellets, frozen tissue) $26 sample
DNA Isolation (cell pellets, frozen tissue) $26 sample
RNA Isolation (FFPE – slides, curls) $31 sample
DNA Isolation (FFPE – slides, curls) $31 sample
BiSulfite conversion $26 sample
Total RNA/microRNA isolation from FFPE sections $47 sample
Bioanalyzer DNA & RNA $47 wafer
Bioanalyzer (user running own chips) $16 wafer
Qubit $11 sample
Covaris shear by Core $31 sample
Covaris shear by User with Core Supplies $16 sample
Covaris shear by User with User Supplies $11 sample

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.

Library Prep

Library typeUnit PriceUnit
Stranded RNA-seq Barcoded Library$206sample
Low Input RNA-seq Barcoded Library$361sample
Small RNA-seq Barcoded Library$361sample
RNA Exome Barcoded Library$361sample
Low Input DNA-seq Barcoded Library$186sample
DNA-seq Barcoded Library$129sample
WGBS libraries$361sample

Ion Torrent S5 Prime Sequencing

Type Price Unit
16s Metagenomics Library prep (16s kit, Ion Frag. Kit, barcode) $47 sample
Oncomine TCR β SR Assay – DNA (T cell) $256 sample
Oncomine TCR β SR Assay – RNA (T cell) $256 sample
Oncomine TCR β LR Assay – RNA (T cell) $230 sample
Oncomine BCR, LR Assay – RNA $245 sample

Ion S5 Prime Sequencing Chips, Single-End Reads Only

 520 chip, 6-10 Million Total Reads $423 chip
 530 chip, 16-20 Million Total Reads $603 chip
 540 chip, 60-80 Million Total Reads $721 chip
 550 chip, 100-130 Million Total Reads $850 chip

Ion s5 Prime Chef + Sequencing Run

 200bpRun for 510, 520, 530 chips  $773  chip
 400bpRun for 510, 520, 530 chips  $1,545  chip
 200bp run ONLY – 540chip  $876  chip
 200bp run ONLY – 550chip  $953  chip

Illumina Novaseq 6000 expedited sequencing by Flowcell type and # of Sequencing Cycles

  Unit Price Unit
 SP 100 cycles $1,159 lane
 SP 200 cycle $1,442 lane
 SP 300 cycles $1,983 lane
 SP 500 cycles $2,833 lane
 S1 100 cycles $2,112 lane
 S1 200 cycles $2,833 lane
 S1 300 cycles $3,399 lane
 S2 100 cycles $3,863 lane
 S2 200 cycles $4,790 lane
 S2 300 cycles $5,099 lane
 S4 35 cycles $2,771 lane
 S4 200 cycles $3,605 lane
 S4 300 cycles $3,863 lane
 XP workflow – 2 lanes $160 lane
 XP workflow – 4 lanes $181 lane
 SP 100 cycles $2,318 flowcell
 SP 200 cycles $2,884 flowcell
 SP 300 cycles $3,966 flowcell
 SP 500 cycles $5,665 flowcell
 S1 100 cycles $4,223 flowcell
 S1 200 cycles $5,665 flowcell
 S1 300 cycles $6,798 flowcell
 S2 100 cycles $7,725 flowcell
 S2 200 cycles $9,579 flowcell
 S2 300 cycles $10,197 flowcell
 S4 35 cycles $11,086 flowcell
S4 200 cycles  $14,420 flowcell
 S4 300 cycles $15,450 flowcell
 XP workflow – 2 lanes $320 flowcell
 XP workflow – 4 lanes $721 flowcell