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Sample GSM565259 Query DataSets for GSM565259
Status Public on Aug 20, 2010
Title Raji 1X
Sample type genomic
 
Channel 1
Source name MIRA-enriched DNA
Organism Homo sapiens
Characteristics cell type: Raji methylated DNA fraction
cycles: 1X WGA
cell line: Raji
Growth protocol DMEM + 10% FBS
Extracted molecule genomic DNA
Extraction protocol Genomic DNA was purified from Raji and H929 were sonicated using a Bioruptor (Diagenode) to generate 200-500 bp fragments. Methylated CpG DNA fragments were enriched from 200 ng of sonicated DNA using the MethylCollector Ultra Kit (Actif Motif) following the manufacturer’s protocol.
Label cy5
Label protocol Input and methylated CpG DNA fragments were amplified (WGA2, Sigma), labeled with Cy3 and Cy5 random nonomers (Trilink Biotechnologies) following NimbleGen’s protocol.
 
Channel 2
Source name Input DNA
Organism Homo sapiens
Characteristics cell type: Raji input DNA
cycles: 1X WGA
cell line: Raji
Growth protocol DMEM + 10% FBS
Extracted molecule genomic DNA
Extraction protocol Genomic DNA was purified from Raji and H929 were sonicated using a Bioruptor (Diagenode) to generate 200-500 bp fragments. Methylated CpG DNA fragments were enriched from 200 ng of sonicated DNA using the MethylCollector Ultra Kit (Actif Motif) following the manufacturer’s protocol.
Label cy3
Label protocol Input and methylated CpG DNA fragments were amplified (WGA2, Sigma), labeled with Cy3 and Cy5 random nonomers (Trilink Biotechnologies) following NimbleGen’s protocol.
 
 
Hybridization protocol Samples were hybridized onto a NimbleGen 2.1M Deluxe Human Promoter Array following NimbleGen’s protocol.
Scan protocol The microarray slides were scanned using the Agilent G2565BA DNA Microarray Scanner. Images were processed using the NimbleScan software.
Description MIRA-chip from Raji
Data processing The log2(Cy5) values were normalized using loess curve fitting conditioning on GC content as described in BMC Bioinformatics 2009, 10:173 doi:10.1186/1471-2105-10-173. These signal values were further quantile normalized to adjust for between sample variations. This method accounts for CG effect and also incorporates cy3 data as following. First we bin all probes according to their GC content defined as a ratio of number of C and G nucleotides to the total number of nucleotides in the probe sequence. We used overall variability in GC content values to compute bin width according to zero-stage rule described by Wand (1997). The bins with fewer probes are then merged to make sure that each bin contains at least 500 probes. Within each bin we use loess regression to predict log2(cy5) values as a smooth function of log2(cy3) values. The residuals (difference between observed and predicted value) from this loess fit are then divided by their mean absolute deviations to compute normalized signal.
 
Submission date Jul 12, 2010
Last update date Jul 13, 2010
Contact name Deepak Mav
Organization name Sciome LLC
Street address 2 Davis Drive
City Research Triangle Park
State/province NC
ZIP/Postal code 27709
Country USA
 
Platform ID GPL10671
Series (1)
GSE22884 DNA methylation prevents CTCF-mediated silencing of the oncogene BCL6 in B cell lymphomas

Data table header descriptions
ID_REF
VALUE Quantile Normalized Loess (GC) Corrected log2(cy5)

Data table
ID_REF VALUE
8076_1_1 2.75388092847967
8076_1_3 0.286330756307689
8076_1_5 1.75844877764136
8076_1_7 1.15981588018790
8076_1_9 0.140578032408929
8076_1_11 -1.18480673515179
8076_1_13 0.812827146925528
8076_1_15 2.17171287594344
8076_1_17 6.01388199154229
8076_1_19 4.82910920112091
8076_1_21 -0.00808446257755581
8076_1_23 -0.0755356338734256
8076_1_25 0.83470024014129
8076_1_27 -0.718938645563684
8076_1_29 6.94864453517226
8076_1_31 1.24935179733871
8076_1_33 2.93330691260212
8076_1_35 7.51179671945296
8076_1_37 1.04923139747171
8076_1_39 -1.19099581535384

Total number of rows: 2173622

Table truncated, full table size 67199 Kbytes.




Supplementary file Size Download File type/resource
GSM565259_532.pair.gz 40.9 Mb (ftp)(http) PAIR
GSM565259_635.pair.gz 40.7 Mb (ftp)(http) PAIR
Processed data included within Sample table

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