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Sample GSM390041 Query DataSets for GSM390041
Status Public on Jan 11, 2010
Title Dmel_adult_H4AcK16_ChIP_male_rep3
Sample type genomic
 
Channel 1
Source name input, Drosophila melanogaster adult male
Organism Drosophila melanogaster
Characteristics gender: male
reference: Input, 5-7 day aged adult flies
Growth protocol Flies were grown at 25°C on standard cornmeal media. Wildtype flies for chromatin immunoprecipitaion were aged for 5-7 days post-eclosion, sexed and flash frozen.
Extracted molecule genomic DNA
Extraction protocol About 0.5 g of sex-sorted adult flies was cross-linked with 1.8% for 20 minutes at room temperature. After washing, the flies were completely homogenized and the cells were disrupted by cell lysis and nuclei lysis. The nuclear extraction was then sheared to 200-1000bp by sonication using a Misonix Sonicator 3000 and the soluble chromatin was collected for IPs. Specific antibodies were added to the chromatin extract for two hours and then were bound to protein A agarose beads at 4°C overnight. After washes and elution, the immunoprecipitated DNA was extracted and purified. DNA amplification was performed using a Ligation-mediated PCR (LM-PCR) protocol from FlyChip (http://www.flychip.org.uk/protocols/chip/lm_pcr.php).
Label Cy3
Label protocol 600 ng of amplified DNA (ChIP enriched DNA or input DNA) were then labeled using the Cy3- or Cy5-labeled random nonamers (Trilink Biosciences, San Diego, USA) with Klenow enzymes.
 
Channel 2
Source name H4AcK16 ChIP, Drosophila melanogaster adult male
Organism Drosophila melanogaster
Characteristics gender: male
test: ChIP, 5-7 day aged adult flies
antibody: H4AcK16
Growth protocol Flies were grown at 25°C on standard cornmeal media. Wildtype flies for chromatin immunoprecipitaion were aged for 5-7 days post-eclosion, sexed and flash frozen.
Extracted molecule genomic DNA
Extraction protocol About 0.5 g of sex-sorted adult flies was cross-linked with 1.8% for 20 minutes at room temperature. After washing, the flies were completely homogenized and the cells were disrupted by cell lysis and nuclei lysis. The nuclear extraction was then sheared to 200-1000bp by sonication using a Misonix Sonicator 3000 and the soluble chromatin was collected for IPs. Specific antibodies were added to the chromatin extract for two hours and then were bound to protein A agarose beads at 4°C overnight. After washes and elution, the immunoprecipitated DNA was extracted and purified. DNA amplification was performed using a Ligation-mediated PCR (LM-PCR) protocol from FlyChip (http://www.flychip.org.uk/protocols/chip/lm_pcr.php).
Label Cy5
Label protocol 600 ng of amplified DNA (ChIP enriched DNA or input DNA) were then labeled using the Cy3- or Cy5-labeled random nonamers (Trilink Biosciences, San Diego, USA) with Klenow enzymes.
 
 
Hybridization protocol Hybridizations of samples to the microarrays were performed at 60°C, followed by washes exactly as described (Parisi M, 2004, Genome Biol 5:R40).
Scan protocol Arrays were scanned on an Axon GenePix 4000B (Molecular Devices Corporation, Sunnyvale, CA) and signal for each array elements were extracted with GenePix v.5.1 image acquisition software (Molecular Devices Corporation).
Description ChIP-chip of H4AcK16 in Drosophila adult male flies
Data processing All microarray data were processed and analyzed in R/Bioconductor. The arrays were median centered (subtracting the weighted median from M-values for each array) and then normalized using quantile normalization based on the input channel as common reference across slides.
 
Submission date Apr 07, 2009
Last update date Apr 25, 2012
Contact name Brian Oliver
E-mail(s) briano@nih.gov
Phone 301-204-9463
Organization name NIDDK, NIH
Department LBG
Lab Developmental Genomics
Street address 50 South Drive
City Bethesda
State/province MD
ZIP/Postal code 20892
Country USA
 
Platform ID GPL20
Series (1)
GSE15593 Sex-dependent and -independent X-chromosome histone modifications in Drosophila melanogaster

Data table header descriptions
ID_REF Probe ID for GPL20 platform
Log2Cy3 normalized Log2 transformed signal intensities from Cy3 channel
Log2Cy5 normalized Log2 transformed signal intensities from Cy5 channel
VALUE normalized Log2 transformed ratio of Cy5/Cy3 signal

Data table
ID_REF Log2Cy3 Log2Cy5 VALUE
1 13.357 13.226 -0.13
2 null null null
3 null null null
4 null null null
5 null null null
6 null null null
7 null null null
8 null null null
9 null null null
10 11.131 10.957 -0.174
11 10.906 10.338 -0.568
12 11.032 10.784 -0.248
13 10.689 9.471 -1.219
14 11.393 11.709 0.316
15 11.47 11.966 0.496
16 11.769 12.35 0.581
17 null null null
18 10.34 6.616 -3.724
19 12.022 12.159 0.138
20 11.257 10.678 -0.579

Total number of rows: 31464

Table truncated, full table size 764 Kbytes.




Supplementary file Size Download File type/resource
GSM390041_174_A.gpr.gz 1.4 Mb (ftp)(http) GPR
GSM390041_B12V0887_B.gpr.gz 1.4 Mb (ftp)(http) GPR
Processed data included within Sample table

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