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Data released on February 05, 2016

Supporting materials for "Whole genome sequence analysis of BT-474 using Complete Genomics’ standard and Long Fragment Read technologies".

Chin, R; Ciotlos, S; Drmanac, R; Gulbahce, N; Li, Z; Liu, S, J; Mao, Q; Peters, B, A; Zhang, R, Y (2016): Supporting materials for "Whole genome sequence analysis of BT-474 using Complete Genomics’ standard and Long Fragment Read technologies". GigaScience Database. http://dx.doi.org/10.5524/100188 RIS BibTeX Text

The cell line BT-474 is a popular cell line for studying the biology of cancer and developing novel drugs. However, there is no published complete genome sequence for this highly utilized scientific resource. In this study we sought to provide a comprehensive and useful data set for the scientific community by generating a whole genome sequence for BT-474. Genomic DNA was isolated from an early passage of the BT-474 cell line and 5 ug was used to generate a 114X coverage whole genome sequence using Complete Genomics’ standard sequencing process. In order to provide additional variant phasing and structural variation data we also processed and analyzed two separate libraries of 5 and 6 individual cells to depths of 99X and 87X, respectively using Complete Genomics’ Long Fragment Read technology (LFR). BT-474 is a highly aneuploid cell line with an extremely complex genome sequence. By generating ~300X total coverage we have generated a much more complete understanding, at the genomic level, of this highly utilized cell line.

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Related manuscripts:

doi:10.1186/s13742-016-0113-x

Accessions (data included in GigaDB):

BioProject: PRJEB10587

Keywords:

Long Fragment Read LFR BT474 WGS breast cancer 

Genomic

http://gigadb.org/images/data/cropped/100188.jpg

Samples: Table Settings

Columns:

Common Name
Scienfic Name
Sample Attributes
Taxonomic ID
Genbank Name

Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
BT474_LFR1_library9606HumanhumanHomo sapiens Alternative accession-ENA:ERS823998
Alternative accession-biosample:SAMEA3516849
Description:Homo sapiens; BT474 whole genome seque...
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BT474_LFR2_library9606HumanhumanHomo sapiens Alternative accession-ENA:ERS823997
Alternative accession-biosample:SAMEA3516848
Description:Homo sapiens; BT474 whole genome seque...
...
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BT474_STD_library9606HumanhumanHomo sapiens Alternative accession-ENA:ERS823996
Alternative accession-biosample:SAMEA3516847
Description:Homo sapiens; BT474 whole genome seque...
...
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Displaying 1-3 of 3 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 
BT474_STD_libraryOtherTSV14.6 MB2016-01-20
BT474_LFR2_libraryOtherTSV0.72 KB2016-01-20
BT474_LFR1_libraryOtherTSV0.7 KB2016-01-20
BT474_STD_librarySequence variantsTSV2.97 MB2016-01-20
BT474_LFR2_librarySequence variantsTSV0.56 KB2016-01-20
BT474_LFR1_librarySequence variantsTSV0.65 KB2016-01-20
BT474_STD_libraryHTMLHTML0.2 KB2016-01-20
BT474_STD_libraryImagePNG1.4 MB2016-01-20
BT474_LFR2_libraryHTMLHTML0.2 KB2016-01-20
BT474_LFR2_libraryImagePNG1.13 MB2016-01-20
Displaying 1-10 of 336 File(s).

History:

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