|
| Status |
Public on Jan 07, 2011 |
| Title |
H3K9ac in asf1-1 cells |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
log. growing cells
|
| Organism |
Schizosaccharomyces pombe |
| Characteristics |
cell type: asf1-1
antibody: H3K9ac
|
| Treatment protocol |
Exponentially growing cells were fixed in 3% paraformaldehyde at 18˚C.
|
| 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 by appropriate antibody: H3K9ac (Upstate). Immunoprecipitated DNA was recovered by incubation with protein A 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 |
log. growing cells
|
| Organism |
Schizosaccharomyces pombe |
| Characteristics |
cell type: asf1-1
antibody: none
|
| Treatment protocol |
Exponentially growing cells were fixed in 3% paraformaldehyde at 18˚C.
|
| 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 by appropriate antibody: H3K9ac (Upstate). Immunoprecipitated DNA was recovered by incubation with protein A 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-v1_107_Sep09 protocol). Signal was normalized by combined rank consistency filtering with LOWES intensity normalization. Background signal was estimated as a median processed signal of 152 oligonucleotides with no homology to S. pombe genome.
|
| |
|
| Submission date |
Nov 24, 2010 |
| Last update date |
Jan 07, 2011 |
| 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 |
GPL8908 |
| Series (2) |
| GSE25597 |
Asf1/HIRA facilitate global histone deacetylation and associate with HP1 to promote nucleosome occupancy at heterochromatic loci (ChIP-chip) |
| GSE25605 |
Asf1/HIRA facilitate global histone deacetylation and associate with HP1 to promote nucleosome occupancy at heterochromatic loci |
|
