Tools and Resources

Center for Cell Circuits tool and resource development

3' RNA-seq

3' RNA-seq is a newly developed sequencing protocol to quantify only transcript ends by fine-tuned 3' sequencing.  End-transcript sequencing requires a relatively low number of cells and reduces by approximately one order of magnitude the sequencing depth necessary to quantify genes at levels comparable to standard poly(A) RNA-seq.
The 3' RNA-seq protocol will be publicly available upon publication of the methodology.

Relevant tools developed prior to establishment of the Center for Cell Circuits


Scripture is a method for transcriptome reconstruction that relies solely on RNA-seq reads and an assembled genome to build a transcriptome ab initio. The statistical methods to estimate read coverage significance are also applicable to other sequencing data. Scripture also has modules for ChIP-seq peak calling.


Trinity, developed at the Broad Institute and the Hebrew University of Jerusalem, represents a novel method for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq data. Trinity combines three independent software modules: Inchworm, Chrysalis, and Butterfly, applied sequentially to process large volumes of RNA-seq reads. Trinity partitions the sequence data into many individual de Bruijn graphs, each representing the transcriptional complexity at at a given gene or locus, and then processes each graph independently to extract full-length splicing isoforms and to tease apart transcripts derived from paralogous genes.


Hi-C is a high-throughput strategy to measure global genome organization and generate genome-wide 3D proximity maps.  This technique allows researchers to decipher the relationship between chromosome organization and genome activity to understand how distal functional elements are brought into close spatial proximity.