|
| Status |
Public on Jan 26, 2012 |
| Title |
T3 5mC |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
T3 5mC (MIRA) enriched samples
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: SCLC tumor
enrichment procedure: 5mC (MIRA)
antibodies/kit information: In Lab purified His-MBD3L1 & GST-MBD2b
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNeasy Blood and Tissue kit (Qiagen; Valencia, CA). Genomic DNA was fragmented by sonication to an average size of ~400 bp using a Sonifier cell disruptor 350 (Branson; Danbury, CT).
|
| Label |
Cy5
|
| Label protocol |
According to standard NimbleGen Protocol
|
| |
|
| Channel 2 |
| Source name |
T3 input DNA
|
| Organism |
Homo sapiens |
| Characteristics |
sample type: input DNA
tissue: SCLC tumor
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNeasy Blood and Tissue kit (Qiagen; Valencia, CA). Genomic DNA was fragmented by sonication to an average size of ~400 bp using a Sonifier cell disruptor 350 (Branson; Danbury, CT).
|
| Label |
Cy3
|
| Label protocol |
According to standard NimbleGen Protocol
|
| |
|
| |
| Hybridization protocol |
According to standard NimbleGen Protocol
|
| Scan protocol |
Follow NimbleScan's default using Agilent Scanner
|
| Description |
5mC profile in T3 sample
|
| Data processing |
Biological replicates were quantile-normalized and arrays were normalized by Nimblegen's recommended method, tukey-biweight. Probe ratios were smoothed for three neighboring probes prior to peak calling. Instead of estimating a cutoff ratio based on a hypothetical normal distribution for non-bound probes (Ringo), a quantile-based approach was chosen to estimate methylation intensities. For this aim, peaks at different quantiles were called, where four probes were above the quantile-based threshold with a distance cutoff of 300 bp. Normalized data is log2 transformed ratios (MIRA/INPUT) after tukey biweight normalization.
|
| |
|
| Submission date |
Jan 25, 2012 |
| Last update date |
Jan 26, 2012 |
| Contact name |
Marc Jung |
| E-mail(s) |
mjung@coh.org
|
| Organization name |
City Of Hope
|
| Department |
Biology
|
| Lab |
Gerd Pfeifer
|
| Street address |
1500 East Duarte Street
|
| City |
Duarte |
| State/province |
CA |
| ZIP/Postal code |
91010 |
| Country |
USA |
| |
|
| Platform ID |
GPL15160 |
| Series (1) |
| GSE35341 |
The DNA methylation landscape of small cell lung cancer |
|
