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Sample GSM183500 Query DataSets for GSM183500
Status Public on Apr 24, 2007
Title ChIP-Chip with anti-Flag antibody, replicate 1 of 2.
Sample type genomic
Source name Cultured Drosophila S2 cells
Organism Drosophila melanogaster
Characteristics Cultured Drosophila S2 cells
Treatment protocol S2 cells were transfected with pMT-Flag-cwo (1.9 ug) or pMT-Flag (1.9 ug) and pCoHygro (0.1 ug, Invitrogen, for selection) using Effectene (QIAGEN) according to the manufacturer’s instructions. Hygromycin-B (300 ug /ml final concentration, Invitrogen) was added 5 days after transfection. After 3 weeks, the established stable cell lines were used for the ChIP assay. 4×10^7 cells were collected and stimulated by copper sulfate to induce fusion genes.
Growth protocol Drosophila S2 cells were maintained in Schneider′s Drosophila medium (Invitrogen) supplemented with 10% FBS (Bioserum) and antibiotics (12.5 U/ml penicillin, 12.5 mg/ml streptomycin; GIBCO).
Extracted molecule genomic DNA
Extraction protocol Cells were harvested 24 h after stimulation. ChIP was then performed according to the previously described method(Yamashita, M. et al. 2002. Identification of a conserved GATA3 response element upstream proximal from the interleukin-13 gene locus. J Biol Chem 277(44): 42399-42408) with some modifications. In this report, we employed Chromatin Immunoprecipitation Assay Kits (Upstate Biotechnology), anti-Flag M2 antibody (SIGMA) and anti-V5 antibody (SIGMA). Protein G-Sepharose (Amersham) was used for precipitation of antibody/protein immune complexes. The resulting precipitated DNA was amplified by adaptor-mediated PCR(Cawley et al. Unbiased mapping of transcription factor binding sites along human chromosomes 21 and 22 points to widespread regulation of noncoding RNAs. Cell 116(4): 499-509) and then fragmented to 50-150 bp by DNase I (Epicentre) in One-Phor-All buffer (Pharmacia). The distribution of fragmented DNA size was verified on a 2% agarose gel.
Label Biotin
Label protocol The fragmented DNA was then end-labeled with GeneChip Labeling Reagent (Affymetrix) by using terminal deoxynucleotidyltransferase (Roche) in TdT buffer (Roche) and CoCl2 (Roche). To prepare the hybridization cocktail, 5 ug of labeled DNA fragment was mixed with final 1x MES, 3 M TMAC, 0.02% Triton (SIGMA), 50 pM Oligo B2, 1×Hybridization Control (Affymetrix), and 100 ug/ul Herring Sperm DNA (Promega).
Hybridization protocol 200 ul Hybridization cocktail was applied to Drosophila genome tiling array (Affymetrix) and hybridized at 45 dC for 18 h with 45 rpm rotation. Stain and wash was executed by Fluidics station 450 with EukGE-WS2 ver.4 program.
Scan protocol Arrays were scanned by GeneChip Scanner 7G (Affymetrix).
Description Data from the chromatin immunoprecipitation with anti-Flag antibody on Drosophila genome tiling array. Replicate no.1 of 2 (Independent sampling).
Data processing Raw data (CEL file) was normalized and analyzed by TileMap (Ji, H. and Wong, W.H. 2005. TileMap: create chromosomal map of tiling array hybridizations. Bioinformatics 21(18): 3629-3636.) with its default parameters (See suplemental file:
Submission date Apr 22, 2007
Last update date Apr 23, 2007
Contact name Rikuhiro G Yamada
Phone +81-78-306-3191
Fax +81-78-306-3194
Organization name RIKEN
Department Center for Developmental Biology
Lab Laboratory for Systems Biology
Street address Minatojima-Minamimachi 2-2-3
City Kobe
State/province Hyogo
ZIP/Postal code 650-0047
Country Japan
Platform ID GPL3923
Series (1)
GSE7569 Chromatin immunoprecipitation (ChIP) assay of CWO protein with Drosophila genome tiling array

Data table header descriptions
ID_REF CHR_POS: chromosome_genomic position
VALUE Normalized by TileMap with the default parameters of the software

Data table
x985_y567_chr2L_89 1.4353205e+01
x986_y567_chr2L_89 1.4353205e+01
x987_y567_chr2L_89 1.4353205e+01
x988_y567_chr2L_89 1.4353205e+01
x989_y567_chr2L_89 1.4353205e+01
x990_y567_chr2L_89 1.4353205e+01
x991_y567_chr2L_89 1.4353205e+01
x992_y567_chr2L_89 1.4353205e+01
x1938_y565_chr2L_89 1.4353205e+01
x1939_y565_chr2L_89 1.4353205e+01
x401_y411_chr2L_158 1.1730219e+01
x2176_y803_chr2L_162 1.2644100e+01
x2177_y803_chr2L_162 1.2644100e+01
x2178_y803_chr2L_162 1.2644100e+01
x2179_y803_chr2L_162 1.2644100e+01
x2180_y803_chr2L_162 1.2644100e+01
x2181_y803_chr2L_162 1.2644100e+01
x2182_y803_chr2L_162 1.2644100e+01
x2183_y803_chr2L_162 1.2644100e+01
x2184_y803_chr2L_162 1.2644100e+01

Total number of rows: 3214785

Table truncated, full table size 115278 Kbytes.

Supplementary file Size Download File type/resource
GSM183500.CEL.gz 45.4 Mb (ftp)(http) CEL

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