The Applied Bioinformatics Laboratories provide noncoding RNA discovery analysis for researchers.  This analysis performs discovery and quantification of novel and annotated long noncoding RNAs using RNA sequencing (RNA-seq) data. It also allows for automatic integration with other sequencing data such as chromatin immunoprecipitation sequencing (ChIP-seq), assay for transposase-accessible chromatin using sequencing (ATAC-seq), and copy-number variations.

Request a Noncoding RNA Discovery Analysis

To request this service from us, please provide the following:

• a sample sheet with the corresponding conditions for the samples
• the organism(s) of the particular study
• the link to the generated FASTQ data (obtained from NYU Langone’s Genome Technology Center or another sequencing facility)

You receive the following from us:

• a comprehensive report
• quality assessment (alignment rates, average number of genes, and transcripts)
• individual bigWig files for visualization using a genome browser
• principal component analysis plot for assessment of sample similarities
• a comprehensive gene expression table (logarithm of fold change, statistics, normalized expression value of each sample, and annotation for each gene)

Additional or Customized Analyses

We also provide the following analyses:

• sgRNA design
• detailed candidate selection guide

Each of these may be subject to an additional charge.

Additional Resources

Below is a link to a computational pipeline that we typically use for our analyses:

• lncRNA-screen pipeline   

The following select publication has used our analyses:

• Trimarchi T, Bilal E, Ntziachristos P, Fabbri G, Dalla-Favera R, Tsirigos A, et al. Genome-wide mapping and characterization of Notch-regulated long noncoding RNAs in acute leukemia. Cell. 2014;158(3):593-606.