|
| Status |
Public on Sep 21, 2010 |
| Title |
H3_Rpb1_60 |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
H3 ChIP from 1ug/ml Rapamycin treated cells
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
condition: 60min after 1ug/ml Rapamycin treatment
strain: AA
antibody: anti-H3
antibody catalog #: ab1791
antibody manufacturer: Abcam
antibody lot #: 940371
|
| Treatment protocol |
Wash twice with water, resuspend cells in YP and incubate for 6hr. Rapamycin was added in the final concentration of 1ug/ml.
|
| Growth protocol |
yeast cells were grown in YPD to OD0.6 before fixed with 1% formaldehyde; or washed twice with water and resuspended in YP, incubated for 6hr. AA strain was grown in YPD to OD0.4 before fixed with 1% formaldehyde, or 1ug/ml rapamycin was added, cells were fixed after 60min incubation.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
chromatin was prepared according to Fax et al. NAR 2008 (http://0-www-ncbi-nlm-nih-gov.brum.beds.ac.uk/pubmed/18765474)
|
| Label |
Biotin-ddATP
|
| Label protocol |
Dnase I treated, 50-100nt DNA was labeled with biotin-ddA
|
| |
|
| Channel 2 |
| Source name |
Input DNA from 1ug/ml Rapamycin treated cells
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
condition: 60min after 1ug/ml Rapamycin treatment
strain: AA
antibody: none
|
| Treatment protocol |
Wash twice with water, resuspend cells in YP and incubate for 6hr. Rapamycin was added in the final concentration of 1ug/ml.
|
| Growth protocol |
yeast cells were grown in YPD to OD0.6 before fixed with 1% formaldehyde; or washed twice with water and resuspended in YP, incubated for 6hr. AA strain was grown in YPD to OD0.4 before fixed with 1% formaldehyde, or 1ug/ml rapamycin was added, cells were fixed after 60min incubation.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
chromatin was prepared according to Fax et al. NAR 2008 (http://0-www-ncbi-nlm-nih-gov.brum.beds.ac.uk/pubmed/18765474)
|
| Label |
Biotin-ddATP
|
| Label protocol |
Dnase I treated, 50-100nt DNA was labeled with biotin-ddA
|
| |
|
| |
| Hybridization protocol |
see GSE23778_Hybri_Tiling_Protocol.pdf for details
|
| Scan protocol |
default settings for Genechip Scanner 3000
|
| Description |
H3 ChIP from 1ug/ml Rapamycin treated cells
|
| Data processing |
data were processed through MAT Johnson et al. PNAS 2006 (http://0-www-ncbi-nlm-nih-gov.brum.beds.ac.uk/pubmed/16895995)
|
| |
|
| Submission date |
Aug 24, 2010 |
| Last update date |
Sep 21, 2010 |
| Contact name |
Xiaochun Fan |
| Organization name |
Harvard Medical School
|
| Department |
Biological Chemistry & Molecular Pharmacology
|
| Lab |
Kevin Struhl
|
| Street address |
220 Longwood Ave.
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
| |
|
| Platform ID |
GPL7250 |
| Series (1) |
| GSE23778 |
Nucleosome depletion in Saccharomyces cerevisiae terminator |
|
