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Sample GSM1714580 Query DataSets for GSM1714580
Status Public on Mar 25, 2016
Title P1_A5_tissue_(Hs35b_P02R_v01)
Sample type genomic
 
Source name jejunum lacking enterocytes
Organism Homo sapiens
Characteristics treatment: mTAG enrichment protocol
individual: 3-3
sample source: Lithuanian University of Health Sciences
age: 28y
Sex: F
snp c/t-13910: TT
tissue: jejunum lacking enterocytes
Treatment protocol Enterocytes were extracted from jejunum surgical samples. For each sample, the remaining tissue also extracted and is referred to as jejunum lacking enterocytes
Extracted molecule genomic DNA
Extraction protocol DNA was extracted with standard phenol chloroform and ethanol preicpitation method
Label biotin
Label protocol GeneChip Double-stranded DNA Terminal Labeling kit (Affymetrix)
 
Hybridization protocol 7 ug ofDNA was hybridized on GeneChip Human Tiling 2.0R Array (B array; Hs35b_P02R) or Mouse Tiling 2.0R Array (A array; Mm35b_P01R) as indicated in ChIP protocol
Scan protocol Arrays were scanned on an Affymetrix GeneChip Scanner 3000 Targeted Genotyping System (GCS 3000 TF system)
Description Sample name: T_3
Enterocytes extracted using Warm Chelating method
Data processing Array Data were quantile normalized and log2 transformed. A probe's center defines a 200bp window. The Tiling array intensities were extracted using R2.15.2 and the bioconductor package "AffyTiling". Probe sequences were re-mapped to Hg19 for human and Mm10 for mouse using mrfast2.6.1.0 with maximum edit distance 0. Probe intensities were then smoothed using a pseudomedian filter with a bandwidth of 401 bp.
*.smooth.txt.gz: tab-delimited text files containing post-processed probe intensities, with columns: chromosome, start, intensity
 
Submission date Jun 18, 2015
Last update date Mar 25, 2016
Contact name Arturas Petronis
Organization name Centre for Addiction and Mental Health
Street address 250 College St Rm606
City Toronto
ZIP/Postal code M5T 1R8
Country Canada
 
Platform ID GPL4911
Series (2)
GSE69972 Chromosome-wide DNA unmethylome profiling examining human chromosomes 2, 9, 19 and mouse chromosomes 1, 9, 19
GSE69979 Epigenetics of lactose intolerance and lactase persistence

Supplementary file Size Download File type/resource
GSM1714580_P1_A5.CEL.gz 24.9 Mb (ftp)(http) CEL
GSM1714580_T_3.hg19.smooth.txt.gz 33.5 Mb (ftp)(http) TXT
Processed data provided as supplementary file

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