Please submit a new request for bioinformatics analysis by completing the SPARC Request.
Select Center for Genomics Medicine, Bioinformatics Core and provide the requested information.
Someone from the BSR will contact you. Please allow 24 hours for a response.
High-Throughput Sequencing Analysis & Systems Level Analyses
All pipelines have on average a two to three week turnaround time. This depends on the size of the study and the volume of work on going. Please allow one business day for an initial response.
Experimental Design Support
Assistance with experimental design, choice of technological platform, data analysis, and data quality control.
Expression Microarray Technology Analysis
Affymetrix and Illumina expression microarray platforms for genome wide analysis of gene expression.
High-Performance Computing Resources for Genomics
Access to High-performance computing (HPCC) resources, systems administration, and infrastructure for data storage, backup, and mining.
Other (Presentations, Manuscripts, Etc.)
Help with presentations, manuscripts, etc.
RNA sequencing also called whole transcriptome sequencing is a technology that uses high throughput sequencing to reveal a snapshot of RNA presence and quantity from a genome at a given moment in time.
MicroRNA sequencing uses high-throughput DNA sequencing to sequence microRNAs, also called miRNAs. miRNA-seq differs from other forms of RNA-seq in that input material is specifically enriched for small RNAs (and requires a different approach).
High-resolution analysis of DNA methylation is possible via ‘bisulfite (BS) conversion’ where DNA treatment with sodium bisulfite under denaturing conditions converts cytosines, but not methylcytosines, into uracil. BS introduces specific changes into DNA that are dependent on the methylation state of individual cytosine residues and coupled to high throughput sequencing provides an assay for methylation status at single-nucleotide resolution.
Targeted Resequencing/Focused Investigation Of Key Genes
With targeted resequencing, a subset of genes or regions of the genome are isolated and sequenced. Data analysis is focused on these specific genomics areas of interest which may include specific genes of interest (custom content) or targets within genes.
Exome sequencing is a technique for sequencing all the protein-coding genes in a genome (known as the exome). It consists of first selecting only the subset of DNA that encodes proteins (known as exons), and then sequencing that DNA using any high throughput DNA sequencing technology.
Chromatin Immunoprecipitation Linked To Massively Parallel Sequencing
ChIP-sequencing, also known as ChIP-seq, is a method used to analyze protein interactions with DNA. ChIP-seq combines chromatin immunoprecipitation (ChIP) with massively parallel DNA sequencing to identify the binding sites of DNA-associated proteins.
Whole Genome Sequencing
Whole-genome sequencing is the most comprehensive method for analyzing the genome allowing characterization of the mutations that drive diseases including cancer.
Metagenomics (16S rRNA Gene Sequencing)
16S ribosomal RNA (rRNA) sequencing is a common amplicon sequencing method used to identify and compare bacteria present within a given sample. 16S rRNA gene sequencing is a well-established method for studying phylogeny and taxonomy of samples from complex microbiomes or environments including the human body.
Reduced Representation Bisulfite Sequencing (RRBS)
Reduced Representation Bisulfite Sequencing (RRBS) is an effective high-throughput technique utilized to analyze the genome-wide methylation profiles on a single nucleotide level. This technique combines restriction enzymes and bisulfite sequencing in order to enrich for the areas of the genome that have a high CpG content.
Systems Level Analyses
Ingenuity Pathway (IPA) Data Analysis
IPA enables researchers to understand complex genomics data at multiple levels by integrating data from a variety of experimental platforms and providing insight into molecular and chemical interactions, cellular phenotypes, and disease processes. IPA facilitates analysis, integration and understanding of data derived from gene expression, microRNA, and SNP microarrays; metabolomics, proteomics, and RNA-Seq experiments.
Varseq Annotation & Analytics
Varseq software (Golden Helix) can easily and quickly annotate complex whole genome data sets, as well as exome and targeted panel variant output. Varseq takes the millions of variants identified in genome and exome sequencing pipelines and narrows them down to potentially disease-causing and clinically relevant variants.
Advaita Gene Ontology, Pathway Analysis
Impact Analysis quickly identifies significantly impacted pathways based on two forms of evidences: Over Representation Analysis, and Accumulated Perturbation Analysis. iPathwayGuide considers type, function and interactions between genes in the pathway at a systems biology level.
The initial consultation is free.
All charges will be disclosed to investigators prior to initiation of work.
Grant writing or editing requests will be subject to chargeback.
The current university approved rate for MUSC investigators is $110 per hour.