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Sample GSM1508889 Query DataSets for GSM1508889
Status Public on Apr 27, 2015
Title rarb_un_rep3
Sample type genomic
 
Channel 1
Source name rarb chIP, KH2 cells, uninduced
Organism Mus musculus
Characteristics tissue: Mouse Embryonic Stem Cells (KH2)
timepoint: uninduced
chip antibody: rarb
chip antibody vendor: Abcam
chip antibody catalog: Ab53161
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 rarb 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 0.733473403
r_chr11.96116275.W 0.169934773
r_chr2.74361173.W 1.257888994
r_chr15.102765561.C 0.087672341
r_krum_pbx2_chr17.34731256.W -0.256679344
r_shil_mll3_chr5.25002801.C -0.074843886
r_chr2.74443692.C 0.352452852
r_cnwy_ino80d_chr1.63156521.W -0.04638824
r_chr15.102631245.C -0.586751871
r_krum_phc1_chr6.122286393.C 0.347387984
r_chr15.102667486.W -0.012803799
r_krum_pknox2_chr9.36950491.W 0.326975495
r_chr11.96053893.W 0.160304081
r_cntrl_chr10.80294081.W -0.107455183
r_krum_bmi1_chr2.18600845.W -0.38178634
r_chr11.96118638.C 0.373609173
r_chr15.102753281.C 0.135841829
r_chr6.52098264.C 0.583307174
r_chr11.96136955.W -1.25990711
r_chr11.96033652.C -0.17957196

Total number of rows: 102946

Table truncated, full table size 3553 Kbytes.




Supplementary file Size Download File type/resource
GSM1508889_252788710058_201103251049_S01_ChIP_105_Jan09_1_2.txt.gz 29.1 Mb (ftp)(http) TXT
GSM1508889_rarb_un_rep3.bw 917.3 Kb (ftp)(http) BW
Processed data included within Sample table
Processed data provided as supplementary file

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