Comment[GEAAccession]	E-GEAD-408
MAGE-TAB Version	1.1
Investigation Title	Methyaltion calling of two breast cancer cell lines from nanopore whole genome methylation sequencing data.
Experiment Description	We performed whole genome sequencing using PromethION sequencer and CpG methylation calling using nanopolish.
Experimental Design	strain or line design
Experimental Factor Name	cell_line
Experimental Factor Type	cell_line
Person Last Name	Suzuki	Seki	Sakamoto	Sequence
Person First Name	Yutaka	Masahide	Yoshitaka	Kashiwa
Person Affiliation	Suzuki Lab  Department of Computational Biology and Medical Sciences Graduate School of Frontier Sciences, The University of Tokyo			
Person Roles	submitter	submitter	submitter	submitter
Public Release Date	2021-03-03
Protocol Name	P-GEAD-707	P-GEAD-708	P-GEAD-709	P-GEAD-710	P-GEAD-711
Protocol Type	sample collection protocol	nucleic acid extraction protocol	nucleic acid library construction protocol	nucleic acid sequencing protocol	normalization data transformation protocol
Protocol Description	MDA-MD-231 and BT-474 are cultured in L15 medium and RPMI medium (FUJIFILM Wako Pure Chemical) containing L-glutamine supplemented with 10% FBS (Corning) and 1X Antibiotic-Antimycotic (Thermo Fisher Scientific), respectively.	Genomic DNA was extracted from cell lines using MagAttract HMW DNA Kit (Qiagen) according to the manufacturer's instructions.	The nanopore sequencing library was prepared from 1.5 ug of genomic DNA using Ligation Sequencing Kit (SQK-LSK109)  (Oxford Nanopore Technologies).	Whole genome sequencing of MDA-MB-231 and BT-474 cell lines using PromethION and flowcell (FLO-PRO002) (Oxford Nanopore Technologies).	PromethION WGS reads were aligned to a human reference genome (GRCh38.p12) by using minimap2 (version 2.16-r922). Then, we extracted the mapping results with over a threshold of mapping quality (20). We indexed fastq data with fast5 data, and called methylation by using nanopolish (version 0.11.1).
SDRF File	E-GEAD-408.sdrf.txt
Comment[AEExperimentType]	methylation profiling by high throughput sequencing
Comment[BioProject]	PRJDB10864
Comment[Last Update Date]	2021-03-03