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

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.
http://www.broadinstitute.org/software/scripture/?q=home

Trinity

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.
http://trinityrnaseq.sourceforge.net/

Hi-C

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.
http://hic.umassmed.edu/welcome/welcome.php