|
| Status |
Public on Mar 21, 2017 |
| Title |
H3K9me2 ChIP in fft3∆ cells_series3 |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
fft3_delta_immunoprecipitated DNA
|
| Organism |
Schizosaccharomyces pombe |
| Characteristics |
genotype: fft3_delta
antibody: H3K9me2
|
| Treatment protocol |
Exponentially growing cells were fixed in 3% paraformaldehyde at 30˚C. For Fft3-GFP ChIP, cells were incubated at 18˚C for 6h prior to fixation with 3% paraformaldehyde followed by treatment with 10mM dimethyl adipimidate
|
| Growth protocol |
Standard conditions were used to produce logarithmically growing cultures in rich media (YEA) at 30˚C.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Fixed cells were lysed with glass-beads, DNA sheared by sonication to 500-1000bp fragments and immunoprecipitated with H3K9dime antibody (Abcam,ab1220) or GFP antibody (Abcam, ab290). Immunoprecipitated DNA was recovered by incubation with protein A/G slurry and reversed-crosslinked at 65˚C.
|
| Label |
Cy5
|
| Label protocol |
ChIP and whole-cell extract DNA was amplified by random-primed PCR and conjugated with Cy5 (ChIP DNA) or Cy3 (whole-cell extract DNA).
|
| |
|
| Channel 2 |
| Source name |
fft3_delta_whole-cell extract
|
| Organism |
Schizosaccharomyces pombe |
| Characteristics |
genotype: fft3_delta
|
| Treatment protocol |
Exponentially growing cells were fixed in 3% paraformaldehyde at 30˚C. For Fft3-GFP ChIP, cells were incubated at 18˚C for 6h prior to fixation with 3% paraformaldehyde followed by treatment with 10mM dimethyl adipimidate
|
| Growth protocol |
Standard conditions were used to produce logarithmically growing cultures in rich media (YEA) at 30˚C.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Fixed cells were lysed with glass-beads, DNA sheared by sonication to 500-1000bp fragments and immunoprecipitated with H3K9dime antibody (Abcam,ab1220) or GFP antibody (Abcam, ab290). Immunoprecipitated DNA was recovered by incubation with protein A/G slurry and reversed-crosslinked at 65˚C.
|
| Label |
Cy3
|
| Label protocol |
ChIP and whole-cell extract DNA was amplified by random-primed PCR and conjugated with Cy5 (ChIP DNA) or Cy3 (whole-cell extract DNA).
|
| |
|
| |
| Hybridization protocol |
Equal amounts of Cy5-labeled ChIP DNA and Cy3-labeled whole-cell extract DNA were mixed and combined with human Cot1 DNA, Agilent Blocking Agent and Agilent Hybridization buffer, and hybridized to high-density microarrays in Agilent SureHyb hybridization chamber for 24 hours at 65˚C, 10 rpm. After hybridization, slides were washed according to Agilent protocol.
|
| Scan protocol |
Scanned on an Agilent G2505B scanner.
|
| Data processing |
Data were extracted using Agilent Feature Extraction Software (CHIP_1105_Oct12 or ChIP_1200_Jun14 protocol). Signal was normalized by combined rank consistency filtering with LOWESS intensity normalization.
|
| |
|
| Submission date |
Oct 18, 2016 |
| Last update date |
Mar 21, 2017 |
| 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) |
| GSE88902 |
Snf2 Family Protein Fft3 Suppresses Nucleosome Turnover to Promote Epigenetic Inheritance of Heterochromatin and Proper Replication of the Genome [H3K9me2 ChIP] |
| GSE88904 |
Snf2 Family Protein Fft3 Suppresses Nucleosome Turnover to Promote Epigenetic Inheritance of Heterochromatin and Proper Replication of the Genome |
|
