top of page
bioinformatics 2.jpg

10x Genomics

Bioinformatics 

Working closely with the Kentucky IdEA Networks of Research Excellence (KY-INBRE) teams, we offer both standard and custom informatics solutions to provide initial data analysis reports from all of our genomics and transcriptomics pipelines. Pricing is project size dependent.

Our most popular analysis services are listed below. Custom analyses are available; contact our team for  information. 

RNA-seq analysis

RNA-seq analysis can be performed for protein coding genes in supported genomes (mouse, human, rat). Non-supported genomes can be analyzed at an additional cost. Comparison between up to 5 experimental groups (15 samples) is included. All raw and processed data is delivered for further, investigator-driven analysis. 

Standard Project Package Includes: Data QC, transcript mapping and quantification, PCA, differential gene expression, and generation of  UCSC custom browser tracks. 

miRNA-seq analysis

Sm

Small RNA analyses, including micro RNAs and long non-coding RNAs, are available. Differential expression of these species can be performed for supported genomes (mouse, human, rat) . Validated target prediction is also performed using miRTarBase and target gene enrichment analysis.

Standard Project Package Includes: Data QC, normalized data matrices, differential expression analysis, including both up- and down-regulated species, and enrichment analysis for target gene prediction. 

Iso-seq analysis

We provide analysis of transcripts resolved using the PacBio IsoSeq method. These results identify splicing variants, alternatively-spliced isoforms, and identification of novel isoforms and genes. Differential isoform usage can be characterized with additional biological IsoSeq replicates and/or integration with short-read RNA-seq reads.  

Standard Project Package Includes: Data QC, analysis of unique genes and isoforms within and across samples, SQANTI classification of isoforms, custom UCSC Genome Browser tracks, isoform usage information (given sufficient replicates)

Other services offered

Additional and custom bioinformatics services are available. We have experience dealing with whole genome metagenomics, m6A methyl-seq, RIP-seq, CLIP-seq, circular RNA (circRNA), de novo transcriptomics, and variant analysis.  Project scope and pricing will be determined on a case-by-case basis. Please contact our team to set up a meeting!

16s Metagenomics

We provide profiling of bacterial metagenomics communities based on the Illumina 16S rRNA amplicon sequencing protocol. Taxanomic resolution is performed within the Qiime environment and denoised with Dada2. A minimum of 10 biological replicates per condition is recommended. Full-length 16S analysis from data generated with SMRT sequencing or nanopore is also provided, at additional cost. 

Standard Project Package Includes: Data QC, alpha and beta diversity analysis, rarefaction curves, compositional differences, and functional analysis.

Single cell scRNA-seq analysis

Single cell clustering and differential gene expression at the single-cell level are provided in conjunction with data produced by the 10xGenomics platforms (multimodal analysis can be performed for additional cost). The analysis  includes predicted cell counts, cell cluster generation, cluster marker identification, and visualization for a limited set of genes.

Standard Project Package Includes: Data QC and CellRanger statistics, cLoupe files, normalization and filtration of data,  UMAP clustering and relevant markers, top differentially expressed genes, and basic trajectory information. 

De novo assembly

De novo genome assembly is available for both prokaryotic and eukaryotic genomes from data generated by both the Illumina and PacBio systems.

 

Standard Project Package Includes: Data QC, consensus assembled genome, assembly statistics, and variant calling (upon request; may involve added project cost).  

What Our Clients Say

Name, Title

"I'm a testimonial. Click to edit me and add text that says something nice about you and your services. Let your customers review you and tell their friends how great you are."
bottom of page