|
| Status |
Public on Jan 08, 2010 |
| Title |
D23_ASH1_exp2 (DM35B_MF_V02) |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
Anti ASH1 (Sanchez-Elsner et al., 2006) ChIP from ML-DmD23-c4 chromatin
|
| Organism |
Drosophila melanogaster |
| Characteristics |
cell line: ML-DmD23-c4
antibody: ASH1, rat mAb (Sanchez-Elsner et al., 2006)
dsrna treatment: none
|
| Growth protocol |
ML-DmD23-c4 cells were grown to a density of 5x10^6 cells/ml in Schneider's medium (Gibco) supplemented with 10% FBS, 10ug/ml insulin, 100U/ml of Penicillin G, 100ug/ml of Streptomycin sulfate and 292 ug/ml of L-glutamine
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Live cells were crosslinked with 1.8% formaldehyde for 10 min at 25C and soluble chromatin prepared as described in Schwartz et al., 2006. ChIP and sample amplification was done as described in Schwartz et al., 2006.
|
| Label |
biotin
|
| Label protocol |
2ug of amplified ChIP product was fragmented with DNAse I and labeled with TdT by biotin-11-ddATP incorporation
|
| |
|
| Channel 2 |
| Source name |
DNA isolated from matching input ML-DmD23-c4 chromatin
|
| Organism |
Drosophila melanogaster |
| Characteristics |
cell line: ML-DmD23-c4
antibody: none
dsrna treatment: none
|
| Growth protocol |
ML-DmD23-c4 cells were grown to a density of 5x10^6 cells/ml in Schneider's medium (Gibco) supplemented with 10% FBS, 10ug/ml insulin, 100U/ml of Penicillin G, 100ug/ml of Streptomycin sulfate and 292 ug/ml of L-glutamine
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Live cells were crosslinked with 1.8% formaldehyde for 10 min at 25C and soluble chromatin prepared as described in Schwartz et al., 2006. ChIP and sample amplification was done as described in Schwartz et al., 2006.
|
| Label |
biotin
|
| Label protocol |
2ug of amplified ChIP product was fragmented with DNAse I and labeled with TdT by biotin-11-ddATP incorporation
|
| |
|
| |
| Hybridization protocol |
Hybridization of labeled DNA was done in 200ul of solution containing 1xMES, 3M TMAC, 40pM oligo B2, 100u/ml sonicated salmon sperm DNA, 0.02% Triton X100 for 18 hours at 45C with 45rpm rotation. Staining and washing was done using EukGE-WS2v4 protocol
|
| Scan protocol |
Arrays were scanned on an Affymetrix Scanner 3000 7G
|
| Description |
ASH1 ChIP, Biological Rep 1-2
|
| Data processing |
The data was median scaled to 100 and the ratio of average ChIP to average Input was computed and smoothed by taking trimmed mean over sliding 675bp window. All operations were performed with TiMAT v2.8.3
The .sgr files were produced with TiMAT v2.8.3 and contain average ChIP/ average Input values smoothed by taking trimmed mean over sliding 675bp window.
|
| |
|
| Submission date |
Sep 19, 2009 |
| Last update date |
Jan 08, 2010 |
| Contact name |
Yuri B Schwartz |
| E-mail(s) |
[email protected]
|
| Organization name |
Rutgers University
|
| Street address |
604 Allison Rd
|
| City |
Piscataway |
| State/province |
NJ |
| ZIP/Postal code |
08854 |
| Country |
USA |
| |
|
| Platform ID |
GPL6016 |
| Series (1) |
| GSE18177 |
Distribution of PcG, TrxG, RNA Pol II and associated histone marks in ML-DmD23-c4 cells |
|
