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Sample GSM1075919 Query DataSets for GSM1075919
Status Public on Mar 14, 2013
Title Monocytes_18
Sample type genomic
 
Source name CD14+ monocytes
Organism Homo sapiens
Characteristics gender: male
slide: 6929689087
array: R05C02
array_name: 6929689087_R05C02
Treatment protocol Monocytes were purified with MACS CD14 Microbeads from Miltenyi.
Extracted molecule genomic DNA
Extraction protocol DNA was extracted with the Sigma Gene Elute Mammalian Genomic DNA miniprep Kit, according to standard instructions.
Label Cy3 and Cy5
Label protocol Standard Illumina Protocol
 
Hybridization protocol bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450k Beadchip using standard Illumina protocol
Scan protocol Beachips were scanned using an iScan
Description SAMPLE_83
CD14+ monocytes
Data processing Raw intesities exported from GenomeStudio software were imported into R and analyzed with the Bioconductor lumi package. Probes on chromosomes X and Y were removed. Probes with a detection P-value > 0.01 exceeding 5% of the samples were also filtered out. Color-bias adjustment and quantile normalization were performed as implemented in lumi. BMIQ correction was applied to beta values to correct for probe type bias.
 
Submission date Feb 01, 2013
Last update date Jun 27, 2017
Contact name Francesco Marabita
E-mail(s) francesco.marabita@ki.se
Organization name Karolinska Institutet
Street address Karolinska University Hospital
City Stockholm
ZIP/Postal code 17176
Country Sweden
 
Platform ID GPL13534
Series (1)
GSE43976 An evaluation of analysis pipelines for DNA methylation profiling using the Illumina Human Methylation 450k platform

Data table header descriptions
ID_REF
VALUE Normalized Beta

Data table
ID_REF VALUE
cg00000029 0.440286992327523
cg00000108 0.989189945045472
cg00000109 0.933035495088345
cg00000165 0.162854896858855
cg00000236 0.658095504959646
cg00000289 0.730443632748577
cg00000292 0.8699968148932
cg00000321 0.199907087051143
cg00000363 0.310880452423745
cg00000622 0.0176531230044154
cg00000658 0.879086793962095
cg00000714 0.124892356831288
cg00000721 0.967261305788287
cg00000734 0.0439850549642123
cg00000769 0.0646885218702899
cg00000807 0.927377111718896
cg00000884 0.943923463843296
cg00000905 0.039708868232415
cg00000924 0.51960173980874
cg00000948 0.912396844320795

Total number of rows: 473097

Table truncated, full table size 13527 Kbytes.




Supplementary file Size Download File type/resource
GSM1075919_6929689087_R05C02_Grn.idat.gz 4.1 Mb (ftp)(http) IDAT
GSM1075919_6929689087_R05C02_Red.idat.gz 4.1 Mb (ftp)(http) IDAT
Processed data included within Sample table
Processed data are available on Series record

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