|
| Status |
Public on Aug 01, 2011 |
| Title |
MDA-MB-231 targeted BS-seq |
| Sample type |
SRA |
| |
|
| Source name |
MDA-MB-231 breast cancer cell line
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Breast
cell line: MDA-MB-231 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 (http://soap.genomics.org.cn/). 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 |
| E-mail(s) |
hshi@augusta.edu
|
| 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 |
|
| Relations |
| SRA |
SRX039418 |
| BioSample |
SAMN00199073 |
