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
Pricing
Package Pricing
| Library Kit & Platform Design | Output / Coverage | Price per sample | |
|---|---|---|---|
| WGS | Kit: 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 | ||
| WES | Kit: 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 RNAseq | Kit: 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 samples | Price 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 Type | Service 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 FFPE | Illumina EPIC human methylation 750, FFPE | $361 |
| Illumina Methylation | Mouse EPIC array multiple of 12 | $340 |
| Genome Restoration | $155 |
Bioinformatics Services
| Project execution | Unit price | Charge 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 type | Unit Price | Unit |
|---|---|---|
| Stranded RNA-seq Barcoded Library | $206 | sample |
| Low Input RNA-seq Barcoded Library | $361 | sample |
| Small RNA-seq Barcoded Library | $361 | sample |
| RNA Exome Barcoded Library | $361 | sample |
| Low Input DNA-seq Barcoded Library | $186 | sample |
| DNA-seq Barcoded Library | $129 | sample |
| WGBS libraries | $361 | sample |
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 |