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Sample GSM612834 Query DataSets for GSM612834
Status Public on Aug 13, 2013
Title S6_2yrs_M_GC
Sample type genomic
 
Channel 1
Source name MIRA-enriched DNA
Organism Homo sapiens
Characteristics sample type: methylated DNA fraction
subject: 6
age: 2
gender: M
cell type: tonsils
cell type: GC
Treatment protocol FACS purified
Growth protocol isolated ex vivo from tonsil
Extracted molecule genomic DNA
Extraction protocol Genomic DNA was purified using Allprep DNA/RNA/protein columns (Qiagen). Purified genomic DNA was 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. 20 ng of input and enriched DNA fractions were amplified twice with WGA2 (Sigma).
Label cy5
Label protocol Amplified input and methylated CpG DNA fragments labeled with Cy3 and Cy5 random nonomers (Trilink Biotechnologies) following NimbleGen’s protocol.
 
Channel 2
Source name Input DNA
Organism Homo sapiens
Characteristics sample type: input DNA
subject: 6
age: 2
gender: M
cell type: GC
Treatment protocol FACS purified
Growth protocol isolated ex vivo from tonsil
Extracted molecule genomic DNA
Extraction protocol Genomic DNA was purified using Allprep DNA/RNA/protein columns (Qiagen). Purified genomic DNA was 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. 20 ng of input and enriched DNA fractions were amplified twice with WGA2 (Sigma).
Label cy3
Label protocol Amplified input and methylated CpG DNA fragments 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 This is GC MIRA-chip sample from subject 6
Data processing The log2(Cy5) values were normalized using Lowess curve fitting conditioning on GC content as described in BMC Bioinformatics 2009, 10:173. These signal values were further quantile normalized to adjust for between sample variations.
The GC Lowess method referred in this fields utilizes both 'log2(Cy3)' and 'log2(Cy5)' values as following:
Classify probes into bins according to CG content (proportion of number of C and G nucleotides in probe sequence)
For each CG content bin (k), we fit lowess regression to predict log2(Cy5)_k value using log2(Cy3)_k value
Compute normalized value = sigma_bar *(observed log2(Cy5)_k - predicted log2(Cy5)_k)/sigma_k, where sigma_k is mean absolute deviation of (observed log2(Cy5)_k - predicted log2(Cy5)_k) and sigma_bar is geometric mean of all sigma_k's.
This normalization corrects for both dye bias and CG bias simultaneously.
 
Submission date Oct 25, 2010
Last update date Aug 13, 2013
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 (2)
GSE24918 B lymphocyte activation induces DNA methylation reprogramming and establishes a common epigenetic signature in memory B and plasma cell compartments [DNA methylation profiling]
GSE24919 B lymphocyte activation induces DNA methylation reprogramming and establishes a common epigenetic signature in memory B and plasma cell compartments

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

Data table
ID_REF VALUE
8076_678_1242 0.417868514735214
8074_568_3044 0.927233610081271
8075_182_1488 0.084154161133824
8075_391_2097 0.372751752448084
8074_876_3752 1.54140825541552
8075_352_1872 0.742581208837523
8075_389_2191 0.186162675628655
8075_676_1620 0.808724980146589
8075_144_1420 0.654089536833742
8076_532_998 -0.117728658345678
8074_80_3006 -0.388232877408929
8075_546_1446 0.119248945977308
8074_243_4089 0.389412100729888
8074_1023_2815 -0.323457937401163
8075_383_2317 0.138712384667424
8075_264_2454 0.921815881491002
8075_378_2148 0.352412964844264
8076_49_933 0.702356792831054
8074_996_4002 0.380436795118203
8074_13_3309 0.247188135222533

Total number of rows: 2173622

Table truncated, full table size 68599 Kbytes.




Supplementary file Size Download File type/resource
GSM612834_S6_GC_532.pair.gz 40.3 Mb (ftp)(http) PAIR
GSM612834_S6_GC_635.pair.gz 40.4 Mb (ftp)(http) PAIR
Processed data included within Sample table

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