NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM390050 Query DataSets for GSM390050
Status Public on Jan 11, 2010
Title Dmel_adult_H3diMeK4_ChIP_male_rep1
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 H3diMeK4 ChIP, Drosophila melanogaster adult male
Organism Drosophila melanogaster
Characteristics gender: male
test: ChIP, 5-7 day aged adult flies
antibody: H3diMeK4
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 H3diMeK4 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 14.374 11.324 -3.05
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 11.639 11.627 -0.012
11 11.139 11.518 0.379
12 11.339 11.426 0.087
13 10.976 10.008 -0.968
14 11.748 11.703 -0.045
15 12.094 11.961 -0.133
16 11.998 12.637 0.639
17 null null null
18 11.118 7.187 -3.931
19 12.291 12.131 -0.16
20 11.731 10.882 -0.849

Total number of rows: 31464

Table truncated, full table size 763 Kbytes.




Supplementary file Size Download File type/resource
GSM390050_176_A.gpr.gz 1.5 Mb (ftp)(http) GPR
GSM390050_B1290889_B.gpr.gz 1.4 Mb (ftp)(http) GPR
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap