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Sample GSM3392719 Query DataSets for GSM3392719
Status Public on Sep 24, 2018
Title Placental-Obese-BioRep1-TechRep1
Sample type genomic
 
Source name Placental-Obese
Organism Homo sapiens
Characteristics gender: Female
sample type: Placental tissue punch
weight: Obese
Extracted molecule genomic DNA
Extraction protocol Total DNA was extracted from frozen tissue (Vanderbilt University Medical Center, Nashville, TN) using a DNeasy Blood and Tissue kit (Qiagen, Valencia, CA).
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 Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting
Description Obese frozen placental punch
Data processing Data was processed with the R packages wateRmelon, methylumi, minfi, and Limma. Probes containing SNPs, a detection p-value of greater than 0.001 in more than 1% of the samples, or a beadcount of less than 3 in 5% of samples were removed. To correct for the differences in probe design, the BMIQ (Beta Mixture Quantile) normiization was used. The function “duplicateCorrelation” was used to account for samples that came from the same patient.
 
Submission date Sep 17, 2018
Last update date Sep 25, 2018
Contact name Kate J Claycombe-Larson
E-mail(s) Kate.Larson@ars.usda.gov
Phone 701-795-8298
Organization name USDA
Department ARS
Lab Nutritional Immunology and Epigenetics
Street address 2420 2nd Avenue North
City Grand Forks
State/province ND
ZIP/Postal code 58203
Country USA
 
Platform ID GPL13534
Series (1)
GSE120062 DNA Methylation data from frozen placental tissue

Data table header descriptions
ID_REF
VALUE normalized BMIQ Average Beta
Detection Pval

Data table
ID_REF VALUE Detection Pval
cg00000029 0.0887658548845142 0
cg00000165 0.609875986474744 0
cg00000236 0.84846155776786 0
cg00000289 0.654426211915951 0
cg00000321 0.442793314246368 0
cg00000363 0.266031326245678 0
cg00000622 0.0264749864056552 0
cg00000658 0.849862822154133 0
cg00000714 0.244717711178137 0
cg00000721 0.935841381926913 0
cg00000734 0.0381625573914125 0
cg00000769 0.0719372793105512 0
cg00000807 0.353815053886585 0
cg00000884 0.523013931415877 0
cg00000905 0.0483348358097508 0
cg00000948 0.710532219288186 0
cg00001099 0.873428026489372 0
cg00001245 0.0270319903037426 0
cg00001249 0.404634942440621 0
cg00001269 0.666422874360076 0

Total number of rows: 391767

Table truncated, full table size 11936 Kbytes.




Supplementary file Size Download File type/resource
GSM3392719_3998888106_R04C01_Grn.idat.gz 4.1 Mb (ftp)(http) IDAT
GSM3392719_3998888106_R04C01_Red.idat.gz 4.2 Mb (ftp)(http) IDAT
Processed data included within Sample table

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