Noncoding RNA Discovery
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.
Below is a link to a computational pipeline that we typically use for our analyses:
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.