Genomics and Epigenomics Shared Resource
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Fees
| Service | Fee for LCCC Members |
| Gene Expression Profiling | |
| Affymetrix | |
| Microarray chip hybridization, staining, washing, and scanning (Partial service) | $140/sample (chip purchased separately) |
| 3' Gene Expression Analysis Full Service (sample preparation, labeling, hybridization, scanning, and basic data analysis*) | $325/sample (chip purchased separately) |
| Arrays including: GeneChip Human Genome U133 Plus 2.0, GeneChipMouse Genome 430A2.0, and GeneChip Rat Genome 230 2.0 | |
| Whole-Transcript Expression Analysis Full Service (sample preparation, labeling, hybridization, scanning, and basic data analysis*) | $365/sample (chip purchased separately) |
| Arrays including Human Exon 1.0 ST Array & Gene1.0 Array for Human, Mouse and Rat. | |
| Agilent | |
| Agilent array scan (hybridization, scanning, and basic data analysis*) | $100/array (arrays purchased separately) |
| Agilent Gene Expression Full Service (sample preparation, labeling, hybridization, scanning, and basic data analysis*) Arrays include 8x60K or 4x44K Human Gene Expression Microarrays |
One-color: $200/array (arrays purchased separately) Two-color: $300/array (arrays purchased separately) |
| ABI | |
| ABI TaqMan Gene Expression assays | $1.5/gene/sample + $60/plate |
| Illumina | |
| Illumina Human HT-12 v4 Expression BeadChip Full Service (sample preparation, labeling, hybridization, scanning, and basic data analysis*) | $125/sample (includes cost of the array) |
| Illumina Mouse WG-6 v2.0 Expression BeadChip Full Service (sample preparation, labeling, hybridization, scanning, and basic data analysis*) | $230/sample (includes cost of the array) |
| Next Generation Sequencing | |
Human Exome Sequencing Full Service (DNA QC, whole-exome capture using the Agilent SureSelect kit v4 (54Mb), library prep, indexing and 100 bp paired-end reads on the Illumina HiSeq2000/2500 (100X coverage). Raw FASTQ seq provided along with standard bioinformatics including reference genome mapping and variant calls. |
$1160/sample |
Human RNA-Seq Full Service (RNA QC (Agilent Bioanalyzer), library preparation (Illumina TruSeq), indexing and 100 bp singleton reads on the Illumina HiSeq2000/2500 (40M reads/sample). Raw FASTQ seq files provided along with standard bioinformatics including differential expression analysis. |
$1425/sample |
De novo Whole-Genome Sequencing, Human Whole-Genome Sequencing, ChIP-Sequencing and Methylation Sequencing, and Custom Targeted Sequencing |
Please inquire for pricing (David Goerlitz, x7 -0832, dsg3@georgetown.edu) |
| DNA Sequencing and Fragment Analysis through GENEWIZ (click to see detailed fee structure and submission instructions) | |
| DNA sequencing (reaction and sequencing) | $5.00/reaction |
| DNA sequencing (sequencing only) | $2.50/reaction |
| Fragment analysis (run only) | $5.00/reaction |
| Fragment analysis (run and data analysis) | $20.00/reaction |
| SNP Genotyping and CNV Analysis | |
| ABI | |
| SNP genotyping by TaqMan real-time PCR | $1.5/gene/sample + $60/plate |
| Illumina | |
| SNP genotyping by Illumina BeadXpress | (Click to see detailed fee structure) |
| Qiagen pyrosequencing | |
| Tri-allelic SNP genotyping by pyrosequencing | $5.00/sample |
| Affymetrix | |
| Genome-Wide Human SNP Array 6.0 Full Service (sample preparation, labeling, hybridization, scanning, and basic data analysis*) | $365/sample (chip purchased separately) |
| Agilent | |
| Agilent array scan (hybridization, scanning, and basic data analysis*) | $100/array (arrays purchased separately) |
| Agilent CGH array Full Service (sample preparation, labeling, hybridization, scanning, and basic data analysis*) | $200/array (arrays purchased separately) |
| DNA Methylation Analysis | |
| Qiagen pyrosequencing | |
| Validation and optimization of new assays (does not include inventoried assays) | $500/assay |
| Methylation analysis by pyrosequencing includes bisulfite modification of DNA | $16.50/sample |
| ABI | |
| Real Time Methylation Specific PCR (RT-MSP) | $1.5/gene/sample + $60/plate |
| Agilent | |
| Agilent array scan (hybridization, scanning, and basic data analysis*) | $100/array (arrays purchased separately) |
| Agilent DNA Methylation array Full Service (sample preparation, labeling, hybridization, scanning, and basic data analysis*) | $200/array (arrays purchased separately) |
| Illumina | |
| Illumina Infinium Human Methylation450 BeadChip Full Service (sample preparation, labeling, hybridization, scanning, and basic data analysis*) | $450/array (includes cost of the array) |
| Methylation by Illumina BeadXpress | 96-plex CpG: $12,902.40 +$250/plate (480 samples) |
| 384-plex CpG: $44,102.40 +$250/plate (480 samples) | |
| (Click to see detailed fee structure) | |
| microRNA Expression Profiling | |
| ABI | |
| miRNA analysis by TaqMan Low Density Array (TLDA) Full Service includes microRNA array, RT-PCR, PCR reaction, and basic data analysis* | $550/sample (includes cost of the array) |
| Affymetrix | |
| GeneChip miRNA 2.0 array Full Service (sample preparation, labeling, hybridization, scanning, and basic data analysis*) | $325/sample (chip purchased separately) |
| Agilent | |
| Agilent Human miRNA array Full Service (sample preparation, labeling, hybridization, scanning, and basic data analysis*) | $350/sample (includes cost of the array) |
| RNA Quality Assessment | |
| RNA quality measurement by Agilent Bioanalyzer | $50/chip |
| DNA/RNA Isolation and Plating and Assay Preparation | |
| DNA/RNA Isolation | $15/sample |
| Plating and Assay preparation | $350/96-well plate (reformat 96 DNA |
| samples in tubes to 96-well deep plate, OD and normalize) | |
| $200/Reformat 4 96-well plates into 384-well plate, plus $6/384-well plate created | |
| siRNA Screening | |
| siRNA Screen (initial consultation and experimental design support, liquid robotic handling in 96- and 384-well plate format) | $2800/screen |
| User Operated Instruments | |
| ABI Sequence Analyzer HT7900 | $20/hr |
| Berthold LB 96 Luminometer | $100/year |
| Tecan Ultra Fluorescence Microplate Reader | $100/year |
| Amaxa Nucleoporator | $100/year |
| Axon GenePix 4000A Scanner | $100/year |
| Alpha Innotech FluoroChem-8900 | $100/year |
| NanoDrop ND-1000 Spectrophotometer | $100/year |
| Beckman DU-640 Spectrophotometer | $100/year |
| BioTek EL-808IU-PC Microplate Reader | $100/year |
| LI-COR Odyssey Infrared Imager | $100/year |
| Advanced Data Analysis** | |
| Avaliable software tools include: | $75/hour |
| R/Bioconductor | |
| Partek Genomics Suite | |
| Agilent GeneSpring | |
| Agilent DNA Analytics (Genomics Workbench) |
|
| Integromics RealTime StatMiner Oncomine Research Premium Edition |
|
| Ingenuity Pathway Analysis (IPA) Tool | |
| *Basic data analysis includes data pre-processing, fold change calculation, statistical significance analysis (p-values), and multiple testing correction (e.g., FDR) | |
| **Advanced data analysis includes gene set enrichment analysis, cluster analysis (heatmaps), network/pathway analysis, principal component anlysis (PCA), etc. | |
| If you have any questions regarding data analysis, please contact James Li (xl35@georgetown.edu or x7-8533) | |
5/17/2013
