|
| Status |
Public on Jun 17, 2015 |
| Title |
HMEC-hTERT_MeDP_input |
| Sample type |
genomic |
| |
|
| Source name |
HMEC-hTERT, sonication
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HMEC-hTERT
protocol: sonication
precipitation: none
methylated dna capture: none
|
| Treatment protocol |
No treatments.
|
| Growth protocol |
HMEC-hTERT and HMLER cell lines were kindly provided by Anne-Pierre Morel (CRCL, Lyon, France). They were cultivated as previously described (Morel et al. PLoS One 2008).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP-chip and MeDP-chip experiments were performed as previously described (Chatagnon et al. Epigenetics 2011), by the ProfileXpert service (Lyon, France) according to AffymetrixTM protocols. Briefly, chromatin fragments were precipitated with anti-MBD2 antibody (Covalab) and a His6-tagged recombinant protein containing 4 MBD domains cloned from MBD1 (Jorgensen et al. Nucleic Acids Research 2006). The DNA fragments from the ChIP and MeDP experiments were amplified by random PCR.
|
| Label |
biotin
|
| Label protocol |
The samples were labelled with the GeneChip WT Double-Stranded DNA Terminal Labelling Kit
|
| |
|
| Hybridization protocol |
Samples were prepared and hybridized to GeneChip Human Tiling 1.0R Array according to Affymetrix specifications.
|
| Scan protocol |
The tiling arrays were scanned using an Affymetrix GeneChip Scanner 3000 TGPLUS according to manufacturer's instruction.
|
| Description |
Control of MeDP in HMEC-hTERT
|
| Data processing |
Data were processed using the R packages aroma.affymetrix with a MatSmoothing of 500bp (as described at http://aroma-project.org/vignettes/MAT-TilingArrayAnalysis) and Repitools. Annotation is in hg18. SGR files are three colmun tab delimited txt files: chromosome, position and score. They are in hg18.
|
| |
|
| Submission date |
Nov 13, 2014 |
| Last update date |
Jun 17, 2015 |
| Contact name |
Robert Dante |
| E-mail(s) |
robert.dante@lyon.unicancer.fr
|
| Phone |
+33478785922
|
| Organization name |
Cancer Research Center of Lyon
|
| Department |
Tumoral escape
|
| Lab |
Dependence Receptor
|
| Street address |
Centre Léon Bérard 28, rue Laennec
|
| City |
LYON cedex |
| ZIP/Postal code |
69373 |
| Country |
France |
| |
|
| Platform ID |
GPL5082 |
| Series (2) |
| GSE63235 |
Dynamics of MBD2 deposition across methylated DNA regions during malignant transformation of human mammary epithelial cells (3) |
| GSE63237 |
Dynamics of MBD2 deposition across methylated DNA regions during malignant transformation of human mammary epithelial cells |
|
