|
| Status |
Public on Sep 18, 2014 |
| Title |
SAMPLE_13_Fetal |
| Sample type |
genomic |
| |
|
| Source name |
Liver
|
| Organism |
Homo sapiens |
| Characteristics |
group: Fetal
agegroup: Fetal
Sex: Male
tissue: liver
slide: 7990895004
array: R02C02
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
genomic DNA was extracted and purified from liver samples using the AllPrep DNA/RNA/Protein Mini kit (QIAgen, Hilden, Germany) according to standard instructions
|
| Label |
Cy5 and Cy3
|
| 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 HiScan Reader using standard recommended Illumina scanner setting
|
| Data processing |
Bioconductor package’s minfi option ‘Raw’ pre-processing was used to convert the intensities from the red and the green channels from the original IDAT files extracted from the HiScanSQ scanner into methylated and unmethylated signals. Beta values were computed using Illumina’s formula [beta = M/(M+U+100)] and normalized using method SWAN. The beta-values were quantile normalized. The probe sequences were mapped to the human genome reference (build hg19); the bisulfite converted probe sequence were mapped to a similarly converted version of the human genome. All probes that mapped uniquely on both genomes with a minimal sequencing identity of 90% were retained. Probes that mapped to CpG sites with SNPs up to 3 bp upstream of the site or mapped to the X/Y chromosomes were discarded.
|
| |
|
| Submission date |
Sep 09, 2014 |
| Last update date |
Sep 18, 2014 |
| Contact name |
Lili Milani |
| E-mail(s) |
lili.milani@ut.ee
|
| Organization name |
Estonian Genome Center, University of Tartu
|
| Street address |
Riia 23b
|
| City |
Tartu |
| ZIP/Postal code |
51010 |
| Country |
Estonia |
| |
|
| Platform ID |
GPL13534 |
| Series (2) |
| GSE61278 |
Epigenome analysis of fetal and adult liver samples |
| GSE61279 |
Transcriptome and Epigenome analysis of fetal and adult liver samples |
|
