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Sample GSM678519 Query DataSets for GSM678519
Status Public on Mar 01, 2012
Title NimbleGen: Human cerebral cortex H1
Sample type genomic
 
Channel 1
Source name MeDIP DNA from human cerebral cortex
Organism Homo sapiens
Characteristics gender: Male
age (year): 40
Treatment protocol Post-mortem brain samples from cerebral cortex were collected
Extracted molecule genomic DNA
Extraction protocol Genomic DNA from cerebral cortex tissues was extracted using DNeasy Blood & Tissue Kit (Qiagen) and fragmented by ultrasonic wave according to the manufacturer’s instructions
Label Cy5
Label protocol Follow standard NimbleGen protocols
 
Channel 2
Source name Input DNA from human cerebral cortex
Organism Homo sapiens
Characteristics gender: Male
age (year): 40
Treatment protocol Post-mortem brain samples from cerebral cortex were collected
Extracted molecule genomic DNA
Extraction protocol Genomic DNA from cerebral cortex tissues was extracted using DNeasy Blood & Tissue Kit (Qiagen) and fragmented by ultrasonic wave according to the manufacturer’s instructions
Label Cy3
Label protocol Follow standard NimbleGen protocols
 
 
Hybridization protocol Follow standard NimbleGen protocols
Scan protocol The Scanning was performed with the Axon GenePix 4000B microarray scanner
Description Human cerebral cortex DNA methylation
Data processing Between array normalization was conducted using Limma package implemented in R, and the probes that were not unique in the respective genomes were removed from the analyses.
 
Submission date Feb 23, 2011
Last update date Mar 01, 2012
Contact name Jinkai Wang
Organization name University of California, Los Angeles
Street address 650 Charles E. Young Drive South, CHS 33-228
City Los Angeles
State/province CA
ZIP/Postal code 90095-7278
Country USA
 
Platform ID GPL9448
Series (2)
GSE27459 Human cerebral cortex DNA methylation by MeDIP-Chip
GSE27461 Genome-wide DNA methylation analyses in the brain reveal four differentially methylated regions between humans and non-human primates

Data table header descriptions
ID_REF
VALUE log2 (MeDIP/Input) ratio

Data table
ID_REF VALUE
CHR10P100019697 -0.871947488
CHR10P100017997 -1.876476232
CHR10P100019097 -1.367405384
CHR10P100018697 -3.231204782
CHR10P100017897 -0.179206696
CHR10P100019797 -2.97445426
CHR10P100018397 -2.485687465
CHR10P100017497 -0.712062394
CHR10P100018897 -0.488787859
CHR10P100019497 -0.501635934
CHR10P100019897 -2.569183429
CHR10P100018197 -0.587486211
CHR10P100020097 -2.389809171
CHR10P100019297 -1.229542424
CHR10P100019597 -2.107092995
CHR10P100018797 -1.738413778
CHR10P100019197 -0.533025254
CHR10P100017597 -0.06793976
CHR10P100019997 -2.273914386
CHR10P100018497 -1.998238426

Total number of rows: 361766

Table truncated, full table size 10174 Kbytes.




Supplementary file Size Download File type/resource
GSM678519_H1_532.pair.gz 6.9 Mb (ftp)(http) PAIR
GSM678519_H1_635.pair.gz 6.8 Mb (ftp)(http) PAIR
Processed data included within Sample table

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