my5C statistics
my5C specifications
Information
Unique identifier | OMICS_15677 |
---|---|
Name | my5C |
Interface | Web user interface |
Restrictions to use | None |
Input data | The 5C region file, the region name, the restriction site, the optimal primer length, the optimal TM, the primer set options, the primer pool description |
Input format | FASTA |
Computer skills | Basic |
Stability | No |
Maintained | No |
Documentation
- Documentation: http://my5c.umassmed.edu/welcome/welcome.php?tab=primers
Maintainer
Publication for my5C
my5C in publications
(5)[…] 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 […]
Software tools for visualizing Hi C data
[…] 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 […]
Analysis of long range interactions in primary human cells identifies cooperative CFTR regulatory elements
[…] 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 […]
Clustering of Tissue Specific Sub TADs Accompanies the Regulation of HoxA Genes in Developing Limbs
[…] 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 […]
The long range interaction landscape of gene promoters
[…] (“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 […]
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