|
| Status |
Public on May 28, 2015 |
| Title |
Bladder tumor UC_0537_1 |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
Input DNA
|
| Organism |
Homo sapiens |
| Characteristics |
hoglund lab uid: UC_0537_1
tissue: Bladder tumor
sjodahl 2012 molecular subtype: MS1a
lauss 2012 epitype: A1
dna extraction method: AllPrep
nimblegen slide id: 514715
sonication batch: S13
ip-batch: M12
wga reamplification batch: 5
who1999 stage simple: Ta
who 1999 grade: 2
Sex: M
fgfr3 mutation: 1
pik3ca mutation: 1
tp53 mutation: 0
|
| Treatment protocol |
MeDIP (WGA)
|
| Growth protocol |
Primary tumor DNA
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted using DNeasy/Allprep (QIAGEN) spin columns acording to manufacturers specifications, 1250ng genomic DNA was subjected to sonication followed by MeDIP (Diagenode), WGA whole genome amplification (Sigma-Aldrich) and WGA2 re-amplification (Sigma-Aldrich), yielding sufficient amounts of DNA for hybridization to Nimblegen arrays. All sample and input reactions were treated in parallel and (where possible) subjected to the same protocol steps.
|
| Label |
Cy5
|
| Label protocol |
According to manufacturers specifications at the Nimblegen genomics facility
|
| |
|
| Channel 2 |
| Source name |
MeDIP DNA
|
| Organism |
Homo sapiens |
| Characteristics |
hoglund lab uid: UC_0537_1
tissue: Bladder tumor
sjodahl 2012 molecular subtype: MS1a
lauss 2012 epitype: A1
dna extraction method: AllPrep
nimblegen slide id: 514715
sonication batch: S13
ip-batch: M12
wga reamplification batch: 5
who1999 stage simple: Ta
who 1999 grade: 2
Sex: M
fgfr3 mutation: 1
pik3ca mutation: 1
tp53 mutation: 0
|
| Treatment protocol |
Input Control (WGA)
|
| Growth protocol |
Primary tumor DNA
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted using DNeasy/Allprep (QIAGEN) spin columns acording to manufacturers specifications, 1250ng genomic DNA was subjected to sonication followed by MeDIP (Diagenode), WGA whole genome amplification (Sigma-Aldrich) and WGA2 re-amplification (Sigma-Aldrich), yielding sufficient amounts of DNA for hybridization to Nimblegen arrays. All sample and input reactions were treated in parallel and (where possible) subjected to the same protocol steps.
|
| Label |
Cy3
|
| Label protocol |
According to manufacturers specifications at the Nimblegen genomics facility
|
| |
|
| |
| Hybridization protocol |
According to manufacturers specifications at the Nimblegen genomics facility
|
| Scan protocol |
According to manufacturers specifications at the Nimblegen genomics facility
|
| Data processing |
Control hybridization probes as well as all probes not mapping to hg18 autosomes were removed and raw intensities were log2 transformed, the resulting individual dye channels were lowess normalized with respect to probe GC content, ratios were formed by subtracting the Cy3 channel intensities from the Cy5 intensities and the resulting matrix was quantile normalized. Replicate probes were median merged and a PCA-based method for removal of technical variation was applied (Lauss et al. 2013, Cancer informatics).
|
| |
|
| Submission date |
Jun 05, 2014 |
| Last update date |
May 29, 2015 |
| Contact name |
Mattias Aine |
| E-mail(s) |
[email protected]
|
| Phone |
+46-46-2220394
|
| Organization name |
Lund University
|
| Department |
Oncology
|
| Lab |
Urothelial Cancer Genomics
|
| Street address |
Klinikgatan 28
|
| City |
Lund |
| ZIP/Postal code |
SE-221 84 |
| Country |
Sweden |
| |
|
| Platform ID |
GPL17148 |
| Series (1) |
| GSE58256 |
Integrative epigenomic analysis of differential DNA methylation in bladder cancer |
|
