|
| Status |
Public on Jul 06, 2012 |
| Title |
postMBT_MeDIP Repl1 |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
postMBT MeDIP ChIP DNA
|
| Organism |
Danio rerio |
| Characteristics |
cell type: Embryonic cells
strain: AB
developmental stage: postMBT, 5.3 hpf, 50% epiboly
antibody: Anti-5-methylcytosine antibody (10 ng/µl)
antibody catalog#: Mab-006-100
antibody vendor: Diagenode
sample preparation protocol: Chorions were removed with 1 mg/ml pronase and embryos washed in egg water. Yolk proteins were removed in a de-yolking buffer, embryos were sedimented and flash-frozen.
|
| Growth protocol |
Fish and embryos grown as per AAALAC certification
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Embryos and sperm were lysed in lysis buffer, proteinase K treated and sonicated with a Bioruptor (Diagenode). DNA was purified by PCI and ethanol precipitation, and treated with RNase. DNA was re-sonicated to 300-1000 bp fragments. MeDIPs were performed using 4 µg DNA and 5 µl (10 ng/µl) 5-methylcytosine antibody. Samples were washed, deproteinized and DNA purified. Input DNA was fragmented and treated as above without any immunoprecipitation. MeDIP and input DNA was amplified (Sigma-Aldrich, WGA2), cleaned up, eluted and processed for array hybridization (Roche-Nimblegen).
|
| Label |
Cy5
|
| Label protocol |
Labeling done by Nimblegen as per normal service protocol
|
| |
|
| Channel 2 |
| Source name |
postMBT MeDIP Input DNA
|
| Organism |
Danio rerio |
| Characteristics |
cell type: Embryonic cells
strain: AB
developmental stage: postMBT, 5.3 hpf, 50% epiboly
antibody: none, input
sample preparation protocol: Chorions were removed with 1 mg/ml pronase and embryos washed in egg water. Yolk proteins were removed in a de-yolking buffer, embryos were sedimented and flash-frozen.
|
| Growth protocol |
Fish and embryos grown as per AAALAC certification
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Embryos and sperm were lysed in lysis buffer, proteinase K treated and sonicated with a Bioruptor (Diagenode). DNA was purified by PCI and ethanol precipitation, and treated with RNase. DNA was re-sonicated to 300-1000 bp fragments. MeDIPs were performed using 4 µg DNA and 5 µl (10 ng/µl) 5-methylcytosine antibody. Samples were washed, deproteinized and DNA purified. Input DNA was fragmented and treated as above without any immunoprecipitation. MeDIP and input DNA was amplified (Sigma-Aldrich, WGA2), cleaned up, eluted and processed for array hybridization (Roche-Nimblegen).
|
| Label |
Cy3
|
| Label protocol |
Labeling done by Nimblegen as per normal service protocol
|
| |
|
| |
| Hybridization protocol |
Hybridization done by Nimblegen as per normal service protocol
|
| Scan protocol |
Scanning done by Nimblegen as per normal service protocol
|
| Data processing |
log2 (MeDIP/Input) with biweight mean of values subtracted
|
| |
|
| Submission date |
Oct 26, 2011 |
| Last update date |
Jul 06, 2012 |
| Contact name |
Philippe Collas |
| Organization name |
University of Oslo
|
| Department |
Institute of Basic Medical Sciences
|
| Street address |
PO Box 1112 Blindern
|
| City |
Oslo |
| ZIP/Postal code |
0317 |
| Country |
Norway |
| |
|
| Platform ID |
GPL10835 |
| Series (1) |
| GSE33236 |
Developmental features of DNA methylation during activation of the embryonic zebrafish genome |
|
