|
| Status |
Public on Mar 28, 2009 |
| Title |
E-4-8h_H3K4Me3_1_of_3_rep_2 |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
ChIP, embryos at 4-8 hours of development, E-4-8h_H3K4Me3_1_of_3_rep_2
|
| Organism |
Drosophila melanogaster |
| Characteristics |
test: ChIP
antibody: H3K4me3
antibody manufacturer: Abcam
antibody catalog number: ab8580
antibody lot number: 411277
tissue: embryos
time point: 4-8 hours of development
replicate: 1_of_3_rep_2
|
| Treatment protocol |
No treatment
|
| Growth protocol |
1. y; bw cn sp flies are cultivated in cages with apple juice agar plates covered with yeast powder. 2. For a 4-8 hours egg laying, new plates are added after a 2hours pre-egglaying at 9 am and flies are allowed to lay eggs for 4 hours. 3. Embryos are collected at 4.45 pm using a filter mesh and a brush. They are rinsed with EWB and cross-linked at 5 pm in 1.8% formaldehyde at room temperature for 15 min.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Drosophila samples are crushed in presence of 1.8% of formaldehyde for 15 minutes. After washing, the material is sonicated for 15 minutes to solubilize the chromatin. After centrifugation, the supernatant containing soluble chromatin is collected for IPs. Specific antibodies are added to the chromatin extract while one aliquot will be treated for DNA extraction corresponding to the reference samples. ChIP are carried overnight at room temperature. Protein A Sepharose beads are used to pull down the chromatin bound antibodies. After washes and finally elution, the DNA corresponding to the IP'd material is extracted and purified. Amplification of the DNA is done by linker-mediated PCR and used for labeling.
|
| Label |
Cy3
|
| Label protocol |
2 ug of amplified IP DNA are used for random primer labeling reaction (invitrogen). Cy3-dCTP is incorporated for the ChIP samples while Cy5-dCTP is incorporated for the Input chromatin sample. After washing of the labeled material on Centricon columns, 5ug of labeled DNA is used for hybridization.
|
| |
|
| Channel 2 |
| Source name |
Input, embryos at 4-8 hours of development, E-4-8h_H3K4Me3_1_of_3_rep_2
|
| Organism |
Drosophila melanogaster |
| Characteristics |
reference: Input
tissue: embryos
time point: 4-8 hours of development
replicate: 1_of_3_rep_2
|
| Treatment protocol |
No treatment
|
| Growth protocol |
1. y; bw cn sp flies are cultivated in cages with apple juice agar plates covered with yeast powder. 2. For a 4-8 hours egg laying, new plates are added after a 2hours pre-egglaying at 9 am and flies are allowed to lay eggs for 4 hours. 3. Embryos are collected at 4.45 pm using a filter mesh and a brush. They are rinsed with EWB and cross-linked at 5 pm in 1.8% formaldehyde at room temperature for 15 min.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Drosophila samples are crushed in presence of 1.8% of formaldehyde for 15 minutes. After washing, the material is sonicated for 15 minutes to solubilize the chromatin. After centrifugation, the supernatant containing soluble chromatin is collected for IPs. Specific antibodies are added to the chromatin extract while one aliquot will be treated for DNA extraction corresponding to the reference samples. ChIP are carried overnight at room temperature. Protein A Sepharose beads are used to pull down the chromatin bound antibodies. After washes and finally elution, the DNA corresponding to the IP'd material is extracted and purified. Amplification of the DNA is done by linker-mediated PCR and used for labeling.
|
| Label |
Cy5
|
| Label protocol |
2 ug of amplified IP DNA are used for random primer labeling reaction (invitrogen). Cy3-dCTP is incorporated for the ChIP samples while Cy5-dCTP is incorporated for the Input chromatin sample. After washing of the labeled material on Centricon columns, 5ug of labeled DNA is used for hybridization.
|
| |
|
| |
| Hybridization protocol |
The hybridization solution is composed of 5 ug each of Cy3- and Cy5-labeled DNA, 50 ug of salmon sperm DNA, Agilent Blocking Agent and Agilent Hyb Buffer. The mixture is heated to 95*C for 3 min and then 37*C for 30 minutes immediately prior to hybridization. Samples are hybridized for 40 hours at 65*C. After hybridization the slides are washed in Agilent Wash Buffer 1 for 5 minutes at room temperature and then in Agilent Wash Buffer 2 for 5 minutes at 31*C.
|
| Scan protocol |
Channel 1 & 2 are for the Agilent arrays are scanned on Agilent's DNA Microarray Scanner G2505B at a resolution of 5 microns. Data is extracted from the images using Agilent's Feature Extraction Software 9.5.3.1.
|
| Description |
ChIP-chip of H3K4me3 in Drosophila embryos at 4-8 hours of development, E-4-8h_H3K4Me3_1_of_3_rep_2
|
| Data processing |
We preprocessed microarray data to normalize it and reduce experimental noise as described in Qi et al. (Qi et al., Nature biotechnology 2006). In short, the raw intensities from each channel was divided by the median intensity from that channel before computing a ratio to arrive at a median adjusted ratio. We further subtracted average value of negative control probes on the array and then added one as a regularization parameter.
|
| |
|
| Submission date |
Mar 25, 2009 |
| Last update date |
Aug 19, 2013 |
| Contact name |
Kevin P. White |
| E-mail(s) |
kpwhite@uchicago.edu
|
| Organization name |
University of Chicago
|
| Department |
Institute for Genomics and Systems Biology
|
| Street address |
900 E. 57th STR. 10th FL.
|
| City |
Chicago |
| State/province |
IL |
| ZIP/Postal code |
60615 |
| Country |
USA |
| |
|
| Platform ID |
GPL6949 |
| Series (2) |
| GSE15292 |
Drosophila at different time points of development: ChIP-chip, ChIP-seq, RNA-seq |
| GSE15424 |
ChIP-chip of H3K4me3 in Drosophila at different time points of development |
|
