|
| Status |
Public on Dec 17, 2014 |
| Title |
PatientB_FFPE_500ng_LIG_BS_8ul |
| Sample type |
genomic |
| |
|
| Source name |
colon adenocarcinoma, FFPE from Patient B
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: colon adenocarcinoma
gender: female
input amount: 500 ng
first processing step: REPLI-g ligase
second processing step: bisulfite modification
assay volume: 8 ul
specimen preservation method: formalin-fixed paraffin-embedded (FFPE)
year of tissue collection: 2004
patient id: B
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
QIAamp DNA FFPE Tissue Kit (QIAGEN Inc., Valencia, CA).
|
| Label |
Cy5 and Cy3
|
| Label protocol |
Standard Illumina Protocol.
|
| |
|
| Hybridization protocol |
Bisulfite-converted DNA was amplified, fragmented and hybridized to Illumina Infinium Human Methylation450 BeadChip using standard Illumina protocol.
|
| Scan protocol |
Arrays were imaged using HiScanSQ System (Illumina, Inc.) using standard recommended Illumina scanner setting.
|
| Description |
PatientB_LIG2
Archived formalin-fixed paraffin-embedded colon adenocarinoma.
|
| Data processing |
R/Bioconductor: DASEN method in the WateRmelon package (version 1.2.2).
|
| |
|
| Submission date |
Jul 02, 2014 |
| Last update date |
Dec 17, 2014 |
| Contact name |
Steven Eschrich |
| E-mail(s) |
Steven.Eschrich@moffitt.org
|
| Organization name |
Moffitt Cancer Center
|
| Department |
Biostatistics & Bioinformatics
|
| Street address |
12902 Magnolia Drive
|
| City |
Tampa |
| State/province |
FL |
| ZIP/Postal code |
33612 |
| Country |
USA |
| |
|
| Platform ID |
GPL13534 |
| Series (1) |
| GSE59038 |
Expanding epigenomics to archived FFPE tissues: An evaluation of DNA repair methodologies |
|
