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Sample GSM659626 Query DataSets for GSM659626
Status Public on Aug 01, 2011
Title MCF7-1 targeted BS-seq
Sample type SRA
Source name MCF7 breast cancer cell line
Organism Homo sapiens
Characteristics tissue: Breast
cell line: MCF7 breast cancer cell line
er status: ER+
tumorgenecity: tumorgenic
Growth protocol Breast cancer cell lines were grown in RPMI1640 media supplemented with 10% FBS.
Extracted molecule genomic DNA
Extraction protocol The genomic library was constructed using Illumina Paired-End DNA Sample Prep Kit according to Manufacturer's protocol. The methylated adaptors sets (part number ME-100-0010) were used instead of the pair-end adaptors came with the Sample prep kit.
Library strategy Bisulfite-Seq
Library source genomic
Library selection RANDOM
Instrument model Illumina Genome Analyzer IIx
Description DNA methylation analysis using bisulfite sequencing
Library selection: Hybrid-selection
Data processing Alignment: The raw bisulfite sequencing reads were first converted to "unmethylated reads" via the conversion of all Cs to Ts in silico. The unmethylated, converted sequencing reads were then aligned to the two copies of in silico converted human reference genome (hg18) using SOAP2 ( The results of both mappings were combined, and any reads mapped against both copies of converted reference were resolved by identifying their strand based on the TCAG ratio and the mapping positions used accordingly
Methylation calculation: The methylation level [(# of methylated)/(# of methylated + # of unmethylated)] was calculated after measuring the amount of methylation (CG->CG) and unmethylation (CG->TG) in the CpG position. Only CpGs that are covered by at least 10 sequencing reads were included.
Submission date Jan 24, 2011
Last update date May 15, 2019
Contact name Huidong Shi
Phone 706-721-6000
Organization name Augusta University
Department Georgia Cancer Center
Lab 2125 K
Street address 1120 15th Street, CN2138
City Augusta
State/province GA
ZIP/Postal code 30912
Country USA
Platform ID GPL10999
Series (1)
GSE26826 Targeted bisulfite sequencing by solution hybrid selection and massively parallel sequencing
SRA SRX039415
BioSample SAMN00199070

Supplementary file Size Download File type/resource
GSM659626_MCF7-1.BED.txt.gz 12.7 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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