my5C

[…] 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 […]

[…] provide robust and informative methods for the interpretation of hi-c data. here, we investigate five tools that can be operated using a web browser or a graphical user interface: hi-browse v1.6 [], my5c [], juicebox v1.5 [], the epigenome browser v40.6 [] and the 3d genome browser [] (table ). these tools do not require programming expertise, and are more readily accessible. we assess […]

[…] clustering of interaction frequencies., dhs and ctcf data sets for the saec (acc. no. gse26328 and gse30263) were downloaded from the geo website at http://www.ncbi.nlm.nih.gov/geo/query/acc. the ‘my5c-primer’ and ‘my5c-heatmap’ bioinformatics tools are found at http://3dg.umassmed.edu/my5cheatmap/heatmap.php., the published 5c data were obtained and visualized using the ucsc genome browser […]

[…] 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 […]

[…] (“distal fragments”) in the encode pilot regions., 5c primers were designed at hindiii restriction sites (aagctt) using 5c primer design tools previously developed and made available online at my5c website (http://my5c.umassmed.edu) . reverse 5c primers were designed for hindiii restriction fragments overlapping a known tss from gencode transcripts, or overlapping a start site […]