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Sample GSM4272930 Query DataSets for GSM4272930
Status Public on Dec 15, 2020
Title MAC_54189_D65, lymph node
Sample type genomic
 
Source name lymph node
Organism Macaca mulatta
Characteristics animal_id: 54189
gender: female
siv infection: Chronic infection
timepoint: D65
tissue: lymph node
cell type: CD4+ T cell
Extracted molecule genomic DNA
Extraction protocol Standard Illumina Protocol
Label Cy3/Cy5
Label protocol Standard Illumina Protocol
 
Hybridization protocol bisulphite converted DNA was amplified, fragmented and hybridised to Infinium Human Methylation 450 K bead arrays (Illumina Inc., San Diego, CA). Processing was done according to the manufacturer’s protocol using an automated pipeline. of bisulfite-treated DNA was analyzed using the Infinium Human Methylation 450 K bead arrays spanning approximately over 480,000 CpG sites/sample (Illumina Inc., San Diego, CA). Processing was done according to the manufacturer’s protocol using an automated pipeline, and the arrays were scanned on an Illumina iScan platform (Illumina Inc., San Diego, CA) established at the Life & Brain Center (Bonn, Germany)
Scan protocol the arrays were scanned on an Illumina iScan platform
Data processing Subset quantile normalization, revised version of Touleimat & tost, Epigenomics 2012
Human Illumina arrays were used for monkey samples. Due to the specificity of probes, the normalized data contains only positions that can be reliably measured in the money species and thus not the expected 450K lines.
 
Submission date Jan 15, 2020
Last update date Dec 15, 2020
Contact name Jorg Tost
E-mail(s) jorgtost@gmail.com
Phone 0033160878423
Organization name CEA-Institut de Genomique, Centre National de Genotypage
Lab Laboratory for Epigenetics & Environment
Street address 2 rue Gaston Cremieux
City Evry
ZIP/Postal code 91000
Country France
 
Platform ID GPL13534
Series (1)
GSE143708 Genome-wide DNA methylation analysis reveals dynamic changes in metabolic and immune-regulatory pathways during uncontrolled SIV infection

Data table header descriptions
ID_REF
VALUE Beta-values (Subset quantile normalization)

Data table
ID_REF VALUE
cg00000029 0.91319593551171
cg00000165 0.0886677628505238
cg00000236 0.877110224804585
cg00000289 0.679224889464261
cg00000321 0.112757926427852
cg00000714 0.79309771152311
cg00000734 0.0345218014375123
cg00000769 0.0997200561704638
cg00000807 0.957769247980878
cg00000924 0.240754505422968
cg00001099 0.955952462434341
cg00001364 0.897575340578262
cg00001446 0.925816211442832
cg00001510
cg00001582
cg00001747 0.0321301007514541
cg00001793 0.806969879505013
cg00002033 0.236644649458224
cg00002080 0.950253370902331
cg00002236 0.026487865872882

Total number of rows: 185085

Table truncated, full table size 4775 Kbytes.




Supplementary file Size Download File type/resource
GSM4272930_9554599023_R04C02_Grn.idat.gz 3.9 Mb (ftp)(http) IDAT
GSM4272930_9554599023_R04C02_Red.idat.gz 4.0 Mb (ftp)(http) IDAT
Processed data included within Sample table
Processed data are available on Series record

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