|
| Status |
Public on Feb 03, 2015 |
| Title |
HCT116_shRNA_TET2_1 |
| Sample type |
genomic |
| |
|
| Source name |
HCT116 cell culture, shRNA to TET2_cell line C_replicate1
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HCT116
treatment: shRNA to TET2
|
| Treatment protocol |
Stable knockdown of TET2 in HCT116 used MISSION shRNA Lentiviral Transduction Particles (SHCLNV-NM_017628, Sigma) following manufacturers instructions and selection with 2ug/ml Puromycin (A11138-03, Life Technologies). For TET2C 10MOI of TRCN0000418976 and for TET2+3 5MOI each of TRCN0000418976 and TRCN0000246258 were used. shRNA control used 10MOI of MISSION pLKO.1-puro Non-Target shRNA Control Transduction Particles (SHC016V-1EA, Sigma).
|
| Growth protocol |
HCT116 cells were maintained in McCoy’s 5A medium supplemented with 10% FBS, penicillin and streptomycin.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was purified by phenol:chloroform extraction.
|
| Label |
Cy5 and Cy3
|
| Label protocol |
Standard Illumina Protocol
|
| |
|
| Hybridization protocol |
bisulphite converted DNA was amplified, fragmented and hybridized to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol
|
| Scan protocol |
Arrays were imaged using a HiScan array scannner using standard recommended Illumina scanner setting
|
| Description |
Sample name: TET_KD_2C_1
|
| Data processing |
Raw Infinium data were filtered by removing low quality data using a detection P-value threshold of 0.05. Cross-reactive probes (i.e. targeting several genomic locations) and probes containing SNPs were filtered out using the extended annotation provided by Price et al. [doi:10.1186/1756-8935-6-4]. Probes associated to X and Y chromosomes were removed from the analysis. Beta-values were computed using the formula Beta-value = M/[U+M] where M and U are the raw “methylated” and “unmethylated” signals, respectively. Beta values were corrected for type I and type II bias using the peak-based correction method [doi: 10.1093/bib/bbt054 and doi: 10.2217/epi.11.105].
|
| |
|
| Submission date |
Nov 18, 2014 |
| Last update date |
Sep 14, 2015 |
| Contact name |
Chandra Chilamakuri |
| E-mail(s) |
datasubmissions@cruk.cam.ac.uk
|
| Organization name |
Cancer Research UK Cambridge Institute
|
| Street address |
Robinson Way
|
| City |
Cambridge |
| ZIP/Postal code |
CB2 0RE |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL13534 |
| Series (2) |
| GSE47592 |
5-hydroxymethylcytosine marks promoters in colon that resist hypermethylation in cancer |
| GSE63421 |
5-hydroxymethylcytosine marks promoters in colon that resist hypermethylation in cancer [Methylation450 Array] |
|
