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Sample GSM382158 Query DataSets for GSM382158
Status Public on Mar 20, 2009
Title E-12-16h_H3K9Me3_1_of_3_rep_1
Sample type genomic
 
Channel 1
Source name ChIP, embryos at 12-16 hours of developments, E-12-16h_H3K9Me3_1_of_3_rep_1
Organism Drosophila melanogaster
Characteristics tissue: embryos
time point: 12-16h
test: ChIP
antibody: H3K9me3
antibody manufacturer: Abcam
antibody catalog number: ab8898
antibody lot number: 422485
replicate: 1_of_3_rep_1
Treatment protocol No treatment
Growth protocol The sequenced Drosophila strain poupulation has been amplified and cultivated in population cages. The egg lay for collecting embryos is done in the cage with apple juice agar plates. Egg lay is done for 4 hours and embryos are collected 12 hours later for chromatin extraction.
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 12-16 hours of developments, E-12-16h_H3K9Me3_1_of_3_rep_1
Organism Drosophila melanogaster
Characteristics tissue: embryos
time point: 12-16h
reference: Input
replicate: 1_of_3_rep_1
Treatment protocol No treatment
Growth protocol The sequenced Drosophila strain poupulation has been amplified and cultivated in population cages. The egg lay for collecting embryos is done in the cage with apple juice agar plates. Egg lay is done for 4 hours and embryos are collected 12 hours later for chromatin extraction.
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 H3K9Me3 in Drosophila embryos at 12-16 hours of developments, E-12-16h_H3K9Me3_1_of_3_rep_1
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 19, 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 (3)
GSE15292 Drosophila at different time points of development: ChIP-chip, ChIP-seq, RNA-seq
GSE15422 ChIP-chip of H3K9me3 in Drosophila at different time points of development
GSE18572 Discrete genomic domains exhibit co-occurrence of H3K9me3 and H3K27me3 histone modifications throughout Drosophila

Data table header descriptions
ID_REF
VALUE Normalized log ratios between the Cy3 channel and the Cy5 channel intensities.

Data table
ID_REF VALUE
121180 0.0165984372858186
33716 -0.400463828743336
157277 -0.466555048242884
206658 0.180025702475951
239126 -0.629882625897035
235304 1.26348315326348
134412 -0.338974606982713
53862 -0.264428159941768
198199 -0.00910933370745359
196182 1.0738624796123
126974 0.045864794404221
151252 0.272513335335523
192607 -0.256254063357304
34113 -0.640716368834739
216057 0.02239414640404
135896 -0.26617229047934
170628 0.0431664313688147
161522 0.151701347088782
114968 0.830577593855671
62641 -0.366952870498804

Total number of rows: 237888

Table truncated, full table size 5783 Kbytes.




Supplementary file Size Download File type/resource
GSM382158.txt.gz 23.6 Mb (ftp)(http) TXT
Processed data included within Sample table

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