|
| Status |
Public on Nov 26, 2012 |
| Title |
ChIP/chip of H3K9me2 in rrp6∆ ago1∆ |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
rrp6∆ ago1∆
|
| Organism |
Schizosaccharomyces pombe |
| Characteristics |
chip antibody: H3K9me2 anti-bory
chip antibody manufacturer: Abcam
chip antibody catalog #: ab1220
genotype: rrp6∆ ago1∆
sample type: ChIPed DNA
|
| Treatment protocol |
Cells are fixed with para-formaldehyde for 30min at room temperature.
|
| Growth protocol |
Yeast cells are cultured under YEA medium. For low glucose condition, yeast cells are cultured under EMM medium containing 0.5% glucose.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Sonicated DNA are immunoprecipitated by using H3K9me2 anti-bory(abcam:ab1220)
|
| Label |
cy5
|
| Label protocol |
1ug of DNA(ChIPed/WCE) are suspended in 5ul of 2Xcoupling buffer (Invitrogen) and mixed with 5ul of cy5(Amersham:PA15101) or cy3(Amersham:PA13101). Coupling reaction lasts 2 hours at room temperature.
|
| |
|
| Channel 2 |
| Source name |
rrp6∆ ago1∆
|
| Organism |
Schizosaccharomyces pombe |
| Characteristics |
genotype: rrp6∆ ago1∆
sample type: DNA from whole cell extract
|
| Treatment protocol |
Cells are fixed with para-formaldehyde for 30min at room temperature.
|
| Growth protocol |
Yeast cells are cultured under YEA medium. For low glucose condition, yeast cells are cultured under EMM medium containing 0.5% glucose.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Sonicated DNA are immunoprecipitated by using H3K9me2 anti-bory(abcam:ab1220)
|
| Label |
cy3
|
| Label protocol |
1ug of DNA(ChIPed/WCE) are suspended in 5ul of 2Xcoupling buffer (Invitrogen) and mixed with 5ul of cy5(Amersham:PA15101) or cy3(Amersham:PA13101). Coupling reaction lasts 2 hours at room temperature.
|
| |
|
| |
| Hybridization protocol |
Hybridyzation mix [37.5ul(containing 500ng of cy5-labeled DNA and 500ng of cy3-labeled DNA), 12.5ul of Human Cot1 DNA(1mg/ml:Invitrogen), 12.5ul of 10x Agilent blocking Agent, 62.5ul of 2x Agilent hybridization buffer(high rpm)] is hybridized to array at 65C for 24 hours.
|
| Scan protocol |
Scanned on an Agilent G2600D scanner
|
| Data processing |
Agilent Feature Extraction Software (version 11.0.1.1) was used for quantifying the image, background subtraction, and normalization.
|
| |
|
| Submission date |
Oct 17, 2012 |
| Last update date |
Nov 26, 2012 |
| Contact name |
Shiv Grewal |
| Phone |
2407607553
|
| Organization name |
NCI
|
| Department |
LBMB
|
| Lab |
Shiv Grewal
|
| Street address |
NCI bldg 37 Rm 6068 9000 Rockville Pike
|
| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20892 |
| Country |
USA |
| |
|
| Platform ID |
GPL6503 |
| Series (2) |
| GSE41642 |
RNAi triggered by specialized machinery silences developmental genes and retrotransposons (ChIP-chip) |
| GSE41643 |
RNAi triggered by specialized machinery silences developmental genes and retrotransposons |
|
