How to Obtain Services & User Fees
Services and Fees
For all questions regarding analyses and charges, please contact Andrew Kossenkov, Ph.D., 215-495-6898.
Wistar & Affiliates
Primary image analysis - base calling
sequence alignment to reference genome, ChIP-SEQ
sequence alignment to reference
RNA, small RNA-SEQ, paired end
Integrated genome annotations
integration with genomic annotations
Sample quality is assessed using Illumina base call summary, IVC plots, error graphs, etc.
Depending on the customer’s selection, the following of analysis stage following will be provided at the end of the analysis:
- Primary Analysis: Sequence file in fastq format with base call summary and quality assessment.
- Secondary Analysis: Alignment file in bed format with summary of alignment, including quality of alignment.
- Tertiary Analysis (single or two sample analysis with background statistical model): UCSC browser up-loadable Peak file in bed format, wiggle file in wiggle file format, enrich region in bed format with summary of peaks.
- Genomic Annotation:
- Peaks annotate to genes; each peak is annotated to closest up and downstream gene.
- Peaks annotate to any other binding sites; each peak is annotated to any other customer suggested binding sites. For this purpose, data will be downloaded from NCBI short read archive and processed as required.
- Two samples’ peak comparison also provided.
All analyses will include detailed description of each stage and summary. At different stages of the analysis, customers will be contacted to discuss the progress.
For Solexa Sequencing analysis, contact Priyankara.
Wistar & Affiliates*
e.g. control vs. experimental
Pairwise comparisons, overlaps between results
4 groups or more
Large projects (>24 hours of work) by consultation
Pre-analysis consult (email/in person) is required before analysis is started.
Microarray data analysis and report include:
- Preprocessing: Data extraction, normalization, filtering
- Quality control: Data issues, technical and sample outlier detection, experimental genes check
- Group comparisons:
- Significant genes
- DAVID functional analysis
- Basic core Ingenuity pathway analysis
- Gene overlap between multi-comparisons
- Result files delivered:
- Raw expression data file
- Normalized expression data file
- Gene list files
- P-values, fold changes, etc.
- Function/pathway enrichment files
- PowerPoint report with results and all steps of the analysis
- Post-analysis meeting to discuss/explain the results
For Microarrays and other Bioinformatic questions, contact Andrew.
Advanced pathway analyses include but are not limited to:
- Biomarkers, toxicity, comparison, new pathway, metabolite analyses
- Search and network growth by target name, drug, or disease
- Integration of transcription factors with gene regulation (available late 2011)
- Combined mRNA and miRNA expression analyses using validated (TarBase) and non-validated targets
- Comprehensive literature overview with molecular relationships by target
- Comprehensive clinical trial matrix within specific target/disease area
Basic training in use of Ingenuity and DAVID will be offered depending on interest.
For Advanced Ingenuity/Biological Network analysis, contact Andrew.