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Data released on December 17, 2015

Supporting single-molecule optical genome mapping data from human HapMap and colorectal cancer cell lines.

Hillmer, A, M; Nagarajan, N; Teo, A, S; Verzotto, D; Yao, F (2015): Supporting single-molecule optical genome mapping data from human HapMap and colorectal cancer cell lines. GigaScience Database. http://dx.doi.org/10.5524/100182 RIS BibTeX Text

Next generation sequencing (NGS) technologies have changed our understanding of the variability of the human genome. However, the identification of genome structural variations based on NGS approaches with read lengths of 35 to 300 bases remains to be a challenge. Single molecule optical mapping technologies allow the analysis of DNA molecules of up to 2 Mb and are very suitable for the identification of large scale genome structural variations and for de novo genome assemblies when combined with short read NGS data. Here we present the optical mapping data of two human genomes: the HapMap cell line GM12878 and the colorectal cancer cell line HCT116.
High molecular weight DNA was obtained by embedding GM12878 and HCT116 cells, respectively, in agarose plugs followed by DNA extraction under mild conditions. We digested genomic DNA with KpnI and analyzed 310,000 and 296,000 DNA molecules (≥ 150 kb and 10 restriction fragments), respectively, per cell line using the Argus optical mapping system. We aligned the maps to the human reference by OPTIMA, a new glocal alignment method, and obtained 6.8x and 5.7x genome coverage, 2.9x and 1.7x more than the coverage obtained with previously available software.

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Related manuscripts:

doi:10.1186/s13742-015-0106-1

Related datasets:

doi:10.5524/100182 IsSupplementTo doi:10.5524/100165

Keywords:

optical mapping genomic mapping glocal alignment overlap alignment map-to-sequence alignment 

Genome-Mapping

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Samples: Table Settings

Columns:

Common Name
Scienfic Name
Sample Attributes
Taxonomic ID
Genbank Name

Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
GM128789606HumanhumanHomo sapiens Alternative names:NA12878
Sex:female
Description:HapMap cell line
HCT1169606HumanhumanHomo sapiens Description:commercially available colerectal canc...
Disease status:colerectal cancer
Sex:male
...
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Displaying 1-2 of 2 Sample(s).

Files: (FTP site) Table Settings

Columns:

File Description
Sample ID
File Type
File Format
Size
Release Date
Download Link
File Attributes

File NameSample IDFile TypeFile FormatSizeRelease Date 
GM12878Optical mapUNKNOWN9.61 MB2015-12-04
GM12878Optical mapUNKNOWN9.7 MB2015-12-04
GM12878Optical mapUNKNOWN11.99 MB2015-12-04
GM12878Optical mapUNKNOWN8.43 MB2015-12-04
HCT116Optical mapUNKNOWN3.29 MB2015-12-04
HCT116Optical mapUNKNOWN1.3 MB2015-12-04
HCT116Optical mapUNKNOWN7.51 MB2015-12-04
HCT116Optical mapUNKNOWN7.88 MB2015-12-04
HCT116Optical mapUNKNOWN7.72 MB2015-12-04
HCT116Optical mapUNKNOWN11.4 MB2015-12-04
Displaying 1-10 of 11 File(s).

History:

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