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Sample GSM1508873 Query DataSets for GSM1508873
Status Public on Apr 27, 2015
Title pol2_un
Sample type genomic
 
Channel 1
Source name pol2 chIP, KH2 cells, uninduced
Organism Mus musculus
Characteristics tissue: Mouse Embryonic Stem Cells (KH2)
timepoint: uninduced
chip antibody: pol2
chip antibody vendor: Santa Cruz Biotechnology, Inc.
chip antibody catalog: Sc889
Extracted molecule genomic DNA
Extraction protocol 37 degrees C for 11 min. Crosslinking was stopped by 1mL 1.25 M glycine to each 10 mL and by incubating at room temperature for 5 min. Cells were sonicated for 25 min in bioruptor at high setting and 30 sec on-off cycle. Input DNA and IP DNA in the amount of 10ng were amplified according to the Agilent Genomic DNA Labeling Kit PLUS (Agilent, 5188-5309, Agilent publication number G4481-90010).
Label Cy5
Label protocol Extracts were labeled according to Agilent Genomic DNA Labeling Kit PLUS (Agilent, 5188-5309, Agilent publication number G4481-90010).
 
Channel 2
Source name pol2 chIP, KH2 cells, uninduced
Organism Mus musculus
Characteristics sample type: input
cell type: KH2 cells
timepoint: uninduced
Extracted molecule genomic DNA
Extraction protocol 37 degrees C for 11 min. Crosslinking was stopped by 1mL 1.25 M glycine to each 10 mL and by incubating at room temperature for 5 min. Cells were sonicated for 25 min in bioruptor at high setting and 30 sec on-off cycle. Input DNA and IP DNA in the amount of 10ng were amplified according to the Agilent Genomic DNA Labeling Kit PLUS (Agilent, 5188-5309, Agilent publication number G4481-90010).
Label Cy3
Label protocol Extracts were labeled according to Agilent Genomic DNA Labeling Kit PLUS (Agilent, 5188-5309, Agilent publication number G4481-90010).
 
 
Hybridization protocol Arrays were hybridized with a mixture of 4µg Cy3 labeled DNA and 4µg Cy5 labeled DNA probes. Hybridizations were performed at 650C for 24 hours under standard conditions (45 mg/mL Human Cot-1 DNA, 1X Agilent blocking agent, and 1X Agilent hybridization buffer) and slides were washed successively with Agilent ChIP wash buffer 1, at room temperature and then Agilent ChIP wash buffer 2, at 31C, prior to scanning.
Scan protocol Microarray images were acquired with an Agilent High-Resolution DNA Microarray Scanner (G2505C). For image analysis Agilent Feature Extraction software (Version 10.5.1.1) was used.
Data processing Agilent tiling arrays were hybridized in a two-color configuration and data was read into R (2.11.1). Data was analyzed using the limma (3.4.3) package. Data was normalized within arrays using loess normalization.
 
Submission date Sep 19, 2014
Last update date Apr 27, 2015
Contact name Madelaine Gogol
Organization name Stowers Institute
Department Computational Biology Core
Street address 1000 E. 50th Street
City Kansas City
State/province MO
ZIP/Postal code 64110
Country USA
 
Platform ID GPL19237
Series (2)
GSE61584 Retinoids induce rapid dynamic changes in the non-coding RNAs and epigenetic profiles of murine Hox clusters (ChIP-chip)
GSE61590 Retinoids induce rapid dynamic changes in the non-coding RNAs and epigenetic profiles of murine Hox clusters

Data table header descriptions
ID_REF
VALUE loess normalized log2(ip/input)

Data table
ID_REF VALUE
r_chr15.102777561.C 0.305029185
r_chr11.96116275.W 1.812799772
r_chr2.74361173.W 1.427897562
r_chr15.102765561.C -0.358829833
r_krum_pbx2_chr17.34731256.W 0.44874598
r_shil_mll3_chr5.25002801.C 0.412527582
r_chr2.74443692.C 0.457547071
r_cnwy_ino80d_chr1.63156521.W 0.501200534
r_chr15.102631245.C 0.669172636
r_krum_phc1_chr6.122286393.C -1.040799183
r_chr15.102667486.W 1.468969949
r_krum_pknox2_chr9.36950491.W 0.635206159
r_chr11.96053893.W 1.070859312
r_cntrl_chr10.80294081.W -0.094672072
r_krum_bmi1_chr2.18600845.W 0.091101392
r_chr11.96118638.C -0.252819941
r_chr15.102753281.C 0.068429439
r_chr6.52098264.C -0.131489252
r_chr11.96136955.W -0.624053277
r_chr11.96033652.C 0.560354165

Total number of rows: 102946

Table truncated, full table size 3551 Kbytes.




Supplementary file Size Download File type/resource
GSM1508873_252788710037_201011041042_S01_ChIP_105_Jan09_1_1.txt.gz 29.3 Mb (ftp)(http) TXT
GSM1508873_pol2_un.bw 912.0 Kb (ftp)(http) BW
Processed data included within Sample table
Processed data provided as supplementary file

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