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Sample GSM558457 Query DataSets for GSM558457
Status Public on Jun 25, 2010
Title WTvsKO NSCs, DNA methylation by MeDIP-chip (2/4), exp1
Sample type genomic
 
Channel 1
Source name KO NSC, immunoprecipitated DNA by 5-methylcytosine antibodies
Organism Mus musculus
Characteristics tissue: postnatal SVZ
genotype/variation: Dnmt3a-null
cell type: neural stem cells
experimental design: IP/IP
Growth protocol postnatal SVZ NSCs were maintained in undifferentiated states in presence of mitogens (10 ng/ml EGF and 10 ng/ml bFGF)
Extracted molecule genomic DNA
Extraction protocol Each ChIP-chip assay was performed with about 20 million cells following Agilent mammalian ChIP-on-chip protocol (March, 2006). Briefly, cells were cross-linked with formaldehyde for 10 min at room temperature. Sonicated chromatin was immunoprecipitated overnight at 4 C with 10 ug immobilized (on 100 ul Dynal protein-G beads, Invitrogen) antibodies to Dnmt3a (Santa Cruz, sc-20703) or H3K27me3 (Millipore, 07-449). MeDIP-chip was perfromed as previously described with minor modifications (Weber et al., 2005). Briefly, 5 ug sonicated, heat-denatured genomic DNA was immunoprecipitated with 5 ul of monoclonal antibody against 5-methylcytidine (Eurogentec) at 4 C overnight. Immunoprecipitated methylated DNA was collected with 30 ul Dynal protein-G beads for 2 h at 4 C.
Label Cy3
Label protocol Whole cell extract and immunoprecipitated DNA were amplified using the Whole Genome Amplification Kit (Sigma), and 5 ug of amplified ChIP/MeDIP or input samples were labeled (5’ Cy5- or Cy3-random nonamers, TriLink Biotechnologies) using the standard protocol (NimbleGen Arrays User’s Guide for ChIP-chip analysis).
 
Channel 2
Source name WT NSC, immunoprecipitated DNA by 5-methylcytosine antibodies
Organism Mus musculus
Characteristics genotype/variation: wild type
cell type: neural stem cells
tissue: postnatal SVZ
experimental design: IP/IP
Growth protocol postnatal SVZ NSCs were maintained in undifferentiated states in presence of mitogens (10 ng/ml EGF and 10 ng/ml bFGF)
Extracted molecule genomic DNA
Extraction protocol Each ChIP-chip assay was performed with about 20 million cells following Agilent mammalian ChIP-on-chip protocol (March, 2006). Briefly, cells were cross-linked with formaldehyde for 10 min at room temperature. Sonicated chromatin was immunoprecipitated overnight at 4 C with 10 ug immobilized (on 100 ul Dynal protein-G beads, Invitrogen) antibodies to Dnmt3a (Santa Cruz, sc-20703) or H3K27me3 (Millipore, 07-449). MeDIP-chip was perfromed as previously described with minor modifications (Weber et al., 2005). Briefly, 5 ug sonicated, heat-denatured genomic DNA was immunoprecipitated with 5 ul of monoclonal antibody against 5-methylcytidine (Eurogentec) at 4 C overnight. Immunoprecipitated methylated DNA was collected with 30 ul Dynal protein-G beads for 2 h at 4 C.
Label Cy5
Label protocol Whole cell extract and immunoprecipitated DNA were amplified using the Whole Genome Amplification Kit (Sigma), and 5 ug of amplified ChIP/MeDIP or input samples were labeled (5’ Cy5- or Cy3-random nonamers, TriLink Biotechnologies) using the standard protocol (NimbleGen Arrays User’s Guide for ChIP-chip analysis).
 
 
Hybridization protocol 34 ug of Cy5- and Cy3-labeled samples were combined and hybridized to each mouse whole genome tiling microarray (Roche/NimbleGen 4-array set) for 16-20 h at 42 ˚C using NimbleGen hybridization System 4.
Scan protocol Microarrays were scanned using the Agilent scanner at 5 micron resolution.
Data processing Data were extracted and analyzed using NimbleScan v2.5 (Roche/NimbleGen). Dnmt3a binding sites were identified by a sliding window-base statistical algorithm in NimbleScan v2.5 (FDR<1% or <5%). For identifying probes associated with a significant increase in H3K27me3 levels or a significant decrease in DNA methylation level in KO NSCs as compared to WT NSCs, a non-parametric one-sided Kolmogorov-Smirno (KS) test was used (KS score>2).
Processed data VALUE definition: Log2 (ch2_signal / ch1_signal)
 
Submission date Jun 21, 2010
Last update date Jun 24, 2010
Contact name Yi Sun
E-mail(s) ysun@mednet.ucla.edu
Phone 310-825-9506
Organization name UCLA
Department Molecular and Medical Pharmacology
Street address 635, Charles E. Young Dr. South
City Los Angeles
State/province CA
ZIP/Postal code 90095
Country USA
 
Platform ID GPL7524
Series (2)
GSE22475 Genome-wide location analysis of Dnmt3a-mediated epigenetic regulation in murine postnatal subventricular zone (SVZ) neural stem cells (NSCs) [NimbleGen]
GSE22476 Dnmt3a-dependent non-promoter DNA methylation facilitates transcription of neurogenic genes

Data table header descriptions
ID_REF
VALUE Log2 (ch2_signal/ch1_signal)

Data table
ID_REF VALUE
CHR04FS119314194 0.42
CHR04FS119314359 -0.84
CHR04FS119314564 0.28
CHR04FS119314755 0.29
CHR04FS119314945 0.52
CHR04FS119315193 0.68
CHR04FS119315362 0.19
CHR04FS119315553 -0.08
CHR04FS119317265 0.27
CHR04FS119317470 -0.37
CHR04FS119317655 0.41
CHR04FS119317880 0.02
CHR04FS119318050 -1.55
CHR04FS119318245 -1.16
CHR04FS119318466 0.50
CHR04FS119318880 0.27
CHR04FS119319061 0.56
CHR04FS119319271 -0.23
CHR04FS119319451 0.38
CHR04FS119319691 0.49

Total number of rows: 2161350

Table truncated, full table size 47500 Kbytes.




Supplementary file Size Download File type/resource
GSM558457_WTvsKO_NSC_MeDIP_array02_exp1_532.pair.gz 42.5 Mb (ftp)(http) PAIR
GSM558457_WTvsKO_NSC_MeDIP_array02_exp1_635.pair.gz 41.2 Mb (ftp)(http) PAIR
GSM558457_WTvsKO_NSC_MeDIP_array02_exp1_log2ratio.txt.gz 11.4 Mb (ftp)(http) TXT
Processed data provided as supplementary file
Processed data included within Sample table

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