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Sample GSM406456 Query DataSets for GSM406456
Status Public on Jan 11, 2010
Title Drosophila_S2_WT_H3diMeK4_ChIP_rep2
Sample type genomic
 
Channel 1
Source name Input, Drosophila melanogaster S2 cells
Organism Drosophila melanogaster
Characteristics cell type: S2 cells
sample type: input
Growth protocol Drosophila S2 cells were grown at 25°C in Schneider's Drosophila Medium (Invitrogen, Carlsbad, CA) supplemented with 10% Fetal Bovine serum (SAFC Biosciences, Lenexa, KS) and Penicillin-Streptomycin.
Extracted molecule genomic DNA
Extraction protocol 5-10 x 106 S2 cells with dsRNA or mock treatment were fixed with 1% formaldehyde in tissue culture media for 10 min at room temperature. After washing, 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 S2 cells
Organism Drosophila melanogaster
Characteristics cell type: S2 cells
antibody: H3diMeK4
Growth protocol Drosophila S2 cells were grown at 25°C in Schneider's Drosophila Medium (Invitrogen, Carlsbad, CA) supplemented with 10% Fetal Bovine serum (SAFC Biosciences, Lenexa, KS) and Penicillin-Streptomycin.
Extracted molecule genomic DNA
Extraction protocol 5-10 x 106 S2 cells with dsRNA or mock treatment were fixed with 1% formaldehyde in tissue culture media for 10 min at room temperature. After washing, 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 S2 WT cells
Data processing All microarray data were processed and analyzed in R/Bioconductor. The arrays were normalized using quantile normalization based on the input channel as common reference across slides.
 
Submission date May 21, 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)
GSE16344 Expression in Aneuploid Drosophila S2 Cells

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 quantile normalized log2 test/input channel

Data table
ID_REF Log2Cy3 Log2Cy5 VALUE
1 15.737 12.319 -3.418
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 10.447 9.557 -0.89
11 11.449 12.941 1.492
12 12.013 11.938 -0.075
13 12.153 14.02 1.867
14 11.942 11.685 -0.258
15 12.942 11.928 -1.015
16 13.649 14.385 0.736
17 null null null
18 12.452 9.51 -2.942
19 13.25 11.598 -1.652
20 12.681 10.407 -2.274

Total number of rows: 31464

Table truncated, full table size 767 Kbytes.




Supplementary file Size Download File type/resource
GSM406456_251_B.gpr.gz 1.5 Mb (ftp)(http) GPR
GSM406456_350_A.gpr.gz 1.5 Mb (ftp)(http) GPR
Processed data included within Sample table

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