Our team have many years of experience with small RNA cloning and analysis, including miRNA/siRNA quantification, 5′ and 3′ heterogeneity, guide/passenger ratio calculation, trimming and tailing detection.

Shown below is the alignments of a small portion of small RNA-Seq against dme-miR-306 hairpin. The alignments, including highlighted mismatches and indels are shown on the left. Reads, frequencies are shown on the right. It is obvious from this analysis that a portion of miR-306 have non-templated nucleotides added to the 3′ ends (aka tailing).

Small RNA-Seq is frequently used to quantify different RNA species. Shown below is a scatter-plot comparing the abundance of piRNAs from different transposon families between two genotypes. The identity of each data point can be found by hovering your mouse on the point. piRNAs aligned to the sense and antisense orientation of the same transposon will be highlighted. You can also turn on/off each piRNA group by clicking the legend square.

We have rich experiences using RNA sequencing for differential expression analysis, de novo and reference-guided transcriptome assembly.

We also offer different variants of RNA-Seq methods, such as GRO-Seq to detect and quantify nascent transcripts, CAGE- and PAS-Seq to identify the transcriptional start and end sites.

We use genomic DNA sequencing to assemble genomes from plasmid and virus to mouse and human. We also have a lot of experiences using genome sequencing to locate integrations of transgene, transposon, and virus in the host genome.

We offer ChIP-Seq analyses including peak-calling, motif discovery, differential representation, as well as publication quality figure generation.