|
| Status |
Public on Jul 01, 2016 |
| Title |
Sh8Day2plus |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
5mC-antibody immunoprecipitation (IP) purified methylated DNA fragments from slincRAD-shRNA8 stable transfected embryo fibroblast 3T3-L1 cell, after adipogenesis on day(+2)
|
| Organism |
Mus musculus |
| Characteristics |
fraction: IP
cell line: 3T3-L1
|
| Treatment protocol |
After cells reached confluence (day 0), cells were induced to differentiate by changing the culture medium to DMEM supplemented with 0.5 mM 3-isobutyl-1-methyxanthine (Sigma),1 μM dexamethasone (Sigma) and 167 nM insulin (Sigma) every two days.
|
| Growth protocol |
Pre-adipocytes 3T3-L1 were cultured in DMEM supplemented with 10% newborn calf serum (Gibco), passaged at 70–80% confluence.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
After Methylated DNA immunoprecipitation (MeDIP) purification, genomic DNA (gDNA) was extracted from samples using a DNeasy Blood & Tissue Kit (Qiagen, Fremont, CA).
|
| Label |
Cy5
|
| Label protocol |
The NimbleGen Dual-Color DNA Labeling Kit was used according to the manufacturer’s guideline detailed in the NimbleGen MeDIP-chip protocol (Nimblegen Systems, Inc., Madison, WI, USA). 1 μg DNA of each sample was incubated for 10 min at 98°C with 1 OD of Cy5-9mer primer (IP sample) or Cy3-9mer primer (Input sample).
|
| |
|
| Channel 2 |
| Source name |
Input of slincRAD-shRNA8 stable transfected embryo fibroblast 3T3-L1 cell, before adipogenesis on day(+2)
|
| Organism |
Mus musculus |
| Characteristics |
fraction: Input
cell line: 3T3-L1
|
| Treatment protocol |
After cells reached confluence (day 0), cells were induced to differentiate by changing the culture medium to DMEM supplemented with 0.5 mM 3-isobutyl-1-methyxanthine (Sigma),1 μM dexamethasone (Sigma) and 167 nM insulin (Sigma) every two days.
|
| Growth protocol |
Pre-adipocytes 3T3-L1 were cultured in DMEM supplemented with 10% newborn calf serum (Gibco), passaged at 70–80% confluence.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
After Methylated DNA immunoprecipitation (MeDIP) purification, genomic DNA (gDNA) was extracted from samples using a DNeasy Blood & Tissue Kit (Qiagen, Fremont, CA).
|
| Label |
Cy3
|
| Label protocol |
The NimbleGen Dual-Color DNA Labeling Kit was used according to the manufacturer’s guideline detailed in the NimbleGen MeDIP-chip protocol (Nimblegen Systems, Inc., Madison, WI, USA). 1 μg DNA of each sample was incubated for 10 min at 98°C with 1 OD of Cy5-9mer primer (IP sample) or Cy3-9mer primer (Input sample).
|
| |
|
| |
| Hybridization protocol |
Microarrays were hybridized at 42°C during 16 to 20h with Cy3/5 labelled DNA in Nimblegen hybridization buffer/ hybridization component A in a hybridization chamber (Hybridization System - Nimblegen Systems, Inc., Madison, WI, USA).
|
| Scan protocol |
Scanned on an Agilent's DNA Microarray scanner and Surescan technology.
|
| Description |
3T3-L1 slincRAD shRNA8 stable transfected cell line, after adipogenesis treated on Day(+2), harvested after several passages.
|
| Data processing |
Median-centering, quantile normalization and linear smoothing were performed in this analysis process by Bioconductor packages Ringo, limma, and MEDME
|
| |
|
| Submission date |
May 23, 2016 |
| Last update date |
Jul 01, 2016 |
| Contact name |
fan yi |
| E-mail(s) |
fanyi0061@163.com
|
| Organization name |
State Key Laboratory of Natural and Biomimetic Drugs
|
| Department |
Peking University
|
| Street address |
Xue Yuan Road 38
|
| City |
Beijing |
| ZIP/Postal code |
100191 |
| Country |
China |
| |
|
| Platform ID |
GPL21852 |
| Series (1) |
| GSE81739 |
Methylation profiling of 3T3-L1 Cells: Control vs slincRAD-shRNA8 stable transfected |
|
