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Sample GSM406459 Query DataSets for GSM406459
Status Public on Jan 11, 2010
Title Drosophila_S2_mof-RNAi-treated_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 mof-RNAi-treated 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 14.329 9.689 -4.64
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 11.426 10.703 -0.723
11 10.632 10.481 -0.152
12 10.925 9.947 -0.979
13 10.873 11.267 0.394
14 12.18 11.495 -0.685
15 12.651 11.666 -0.985
16 12.256 11.903 -0.352
17 null null null
18 10.963 7.715 -3.247
19 12.416 11.458 -0.958
20 11.629 9.904 -1.726

Total number of rows: 31464

Table truncated, full table size 770 Kbytes.




Supplementary file Size Download File type/resource
GSM406459_245_B.gpr.gz 1.5 Mb (ftp)(http) GPR
GSM406459_344_A.gpr.gz 1.5 Mb (ftp)(http) GPR
Processed data included within Sample table

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