|
| 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 |
|
