my5C

[…] ction of the spatial chromatin looping contacts and identification of TADs [, ]. For the 5C analysis, 381 forward and 382 reverse 5C probes were designed in an alternating scheme using the tools from my5C software suite [] to interrogate HindIII sites with the unique anchoring regions at the EDC and its flanking regions (mm9, chromosome 3: 89.9–95.2 Mbp) (, ). The designed probe pool interrogated […]

[…] olutions that strike a balance between sparsity and detail. We found that Juicebox, the Epigenome Browser and the 3D Genome Browser process user data in binary formats in a few seconds. Hi-Browse and my5C do not support loading of a complete dataset at these resolutions, instead the user must upload the Hi-C contact matrix corresponding to the region of interest. The average times required to visu […]

[…] instance of Galaxy as previously described (,). This analysis generates an excel sheet containing interaction frequency lists (IFL) as well as a text file, which was used to visualize results using ‘my5C-heatmap’ ().Normalization between different libraries was done first by read count and then using the compaction profiles for the ERCC3 region and the gene desert region ENr313, setting one sampl […]

[…] ds which do not contain EcoRI restriction sites. This analysis generates an excel sheet containing interaction frequency lists (IFL) as well as a text file, which was used to visualize results using ‘my5C-heatmap’ . Limb-enriched 5C interactions were obtained by subtracting limb and head 5C-seq data. Data was normalized by dividing the number of reads of each 5C contact by the total number of read […]

[…] We used this new analysis platform to obtain normalized interaction frequency values for all pairwise interactions in the HoxA locus and control gene desert region, and visualized the data with the ‘my5C’ heatmap tool (). Figure 2.A shows the HoxA 5C maps from our main time course (biological 1) and from a biological replicate (biological 2) in heatmap form where pairwise IFs are color-coded acco […]

[…] start sites across chromosome 21 and selected domains throughout the genome. Special interfaces have been developed to visualize these 3-dimensional genomic data and are publicly available at http://my5C.umassmed.edu . […]