NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM1508893 Query DataSets for GSM1508893
Status Public on Apr 27, 2015
Title rarg_24_rep2
Sample type genomic
 
Channel 1
Source name rarg chIP, KH2 cells, 24 hrs RA
Organism Mus musculus
Characteristics tissue: Mouse Embryonic Stem Cells (KH2)
timepoint: 24 hrs after RA
chip antibody: rarg
chip antibody vendor: Abcam
chip antibody catalog: Ab97569
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 rarg chIP, KH2 cells, 24 hrs RA
Organism Mus musculus
Characteristics sample type: input
cell type: KH2 cells
timepoint: 24 hrs after RA
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 -0.170216711
r_chr11.96116275.W 0.543217369
r_chr2.74361173.W -0.157690027
r_chr15.102765561.C 0.242957018
r_krum_pbx2_chr17.34731256.W 0.343957557
r_shil_mll3_chr5.25002801.C -0.096784701
r_chr2.74443692.C 0.381850182
r_cnwy_ino80d_chr1.63156521.W -0.175861702
r_chr15.102631245.C -0.320083927
r_krum_phc1_chr6.122286393.C -0.964401595
r_chr15.102667486.W 0.911249004
r_krum_pknox2_chr9.36950491.W -0.231552263
r_chr11.96053893.W -0.215572866
r_cntrl_chr10.80294081.W 0.192249829
r_krum_bmi1_chr2.18600845.W 0.236098044
r_chr11.96118638.C 0.305074233
r_chr15.102753281.C 0.086545502
r_chr6.52098264.C 0.607775965
r_chr11.96136955.W 0.159412211
r_chr11.96033652.C 0.711039232

Total number of rows: 102946

Table truncated, full table size 3553 Kbytes.




Supplementary file Size Download File type/resource
GSM1508893_252788710060_201103251105_S01_ChIP_105_Jan09_1_2.txt.gz 29.1 Mb (ftp)(http) TXT
GSM1508893_rarg_24_rep2.bw 916.8 Kb (ftp)(http) BW
Processed data included within Sample table
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap
External link. Please review our privacy policy.