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Sample GSM1508883 Query DataSets for GSM1508883
Status Public on Apr 27, 2015
Title rara_un_rep2
Sample type genomic
 
Channel 1
Source name rara chIP, KH2 cells, uninduced
Organism Mus musculus
Characteristics tissue: Mouse Embryonic Stem Cells (KH2)
timepoint: uninduced
chip antibody: rara
chip antibody vendor: Abcam
chip antibody catalog: Ab28767
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 rara 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 0.193495307
r_chr11.96116275.W 0.360883463
r_chr2.74361173.W 0.720505167
r_chr15.102765561.C 0.48231256
r_krum_pbx2_chr17.34731256.W 0.066519011
r_shil_mll3_chr5.25002801.C 0.156526135
r_chr2.74443692.C 0.30335754
r_cnwy_ino80d_chr1.63156521.W 0.229861731
r_chr15.102631245.C -1.128055119
r_krum_phc1_chr6.122286393.C 0.161468245
r_chr15.102667486.W -0.207143175
r_krum_pknox2_chr9.36950491.W 0.285065374
r_chr11.96053893.W 0.011194098
r_cntrl_chr10.80294081.W -0.081996826
r_krum_bmi1_chr2.18600845.W 0.231582238
r_chr11.96118638.C 0.323773309
r_chr15.102753281.C -0.095264364
r_chr6.52098264.C 0.603030732
r_chr11.96136955.W -0.801368222
r_chr11.96033652.C -0.101006689

Total number of rows: 102946

Table truncated, full table size 3554 Kbytes.




Supplementary file Size Download File type/resource
GSM1508883_252788710049_201012101230_S01_ChIP_105_Jan09_1_1.txt.gz 29.0 Mb (ftp)(http) TXT
GSM1508883_rara_un_rep2.bw 916.7 Kb (ftp)(http) BW
Processed data included within Sample table
Processed data provided as supplementary file

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