|
| Status |
Public on Dec 31, 2014 |
| Title |
8948T_MBDCap-Seq |
| Sample type |
SRA |
| |
|
| Source name |
Human tumour breast tissue
|
| Organism |
Homo sapiens |
| Characteristics |
tissue type: Triple negative breast cancer (TNBCs)
|
| Growth protocol |
DNA was extracted from cells microdissected from human tissue samples representing normal breast and tumor breast tissue.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
The MethylMinerTM Methylated DNA Enrichment Kit (Invitrogen) was used to isolate methylated DNA from 500 ng – 1 μg of genomic FFPET DNA.
10ng DNA of MBDCap enriched DNA was prepared for Ilumina sequencing using the Illumina ChIP-Seq DNA sample prep kit (IP-102-1001) according to the manufacturer’s instructions. The library preparation was analyzed on Agilent High Sensitivity DNA 1000 Chip.
|
| |
|
| Library strategy |
MBD-Seq |
| Library source |
genomic |
| Library selection |
MBD2 protein methyl-CpG binding domain |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Description |
MBDCap-Seq
|
| Data processing |
Sequenced reads were aligned to hg18 genome assembly using bowtie. Reads with more than three mismatches and reads mapping to multiple positions were removed. Finally, multiple reads mapping to exactly the same genomic coordinate were eliminated and only one read was retained for downstream analysis.
For each MBDCap-Seq sample, fragment length was estimated using HOMER software, sequenced tags were shifted to the middle of estimated fragment lenght and the number of sequenced tags overlapping SssI regions was computed.
Genome_build: hg18
Supplementary_files_format_and_content: Text files contain genomic coordinates of SssI regions and the number of overlapping sequenced tags.
|
| |
|
| Submission date |
May 28, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Aaron Statham |
| E-mail(s) |
a.statham@garvan.org.au
|
| Organization name |
Garvan Institute of Medical Research
|
| Department |
Cancer Department
|
| Lab |
Epigenetics Research Laboratory
|
| Street address |
384 Victoria St
|
| City |
Darlinghurst |
| State/province |
NSW |
| ZIP/Postal code |
2010 |
| Country |
Australia |
| |
|
| Platform ID |
GPL10999 |
| Series (1) |
| GSE58020 |
Methylome sequencing identifies potential epigenetic prognostic biomarker signature that stratifies triple negative breast cancer |
|
| Relations |
| BioSample |
SAMN02800957 |
| SRA |
SRX554604 |
