|
| Status |
Public on Jan 10, 2019 |
| Title |
genomic DNA from myofibroblasts ATM1 derived from patient-matched adjacent tissue A1N |
| Sample type |
genomic |
| |
|
| Source name |
ATM1
|
| Organism |
Homo sapiens |
| Characteristics |
gender: Female
patient: P1
sample_group: ATM
|
| Growth protocol |
Primary myofibroblast cultures were maintained in Dulbecco’s Modified Eagle’s Medium (DMEM) supplemented with 10% Fetal Bovine Serum (FBS), 1% penicillin-streptomycin, 1% antibiotic-antimycotic and 1% non-essential amino acid solution. Medium was replaced routinely every 48–60 hours and cells were lysed at 80-90% confluence for DNA extraction.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was purified using a standard phenol/chloroform extraction method.
|
| Label |
Cy5 and Cy3
|
| Label protocol |
standard Illumina protocol
|
| |
|
| Hybridization protocol |
standard Illumina protocol
|
| Scan protocol |
standard Illumina protocol
|
| Description |
adjacent tissue
|
| Data processing |
Raw DNA methylation data were processed and analysed using Bioconductor package RnBeads version 0.99.17 (Assenov, Muller et al. 2014). Prior to normalization, probes with p-value>0.01 in any sample and probes overlapping with single nucleotide polymorphisms (SNPs) in the probe sequence (Chen, Lemire et al. 2013) were removed followed by BMIQ normalization (Teschendorff, Marabita et al. 2013, Wu, Joubert et al. 2014) and methylumi.noob background subtraction (Triche, Weisenberger et al. 2013). Subsequently probes outside of CpG context as well as probes on sex chromosomes were removed.
|
| |
|
| Submission date |
Apr 12, 2017 |
| Last update date |
Jan 11, 2019 |
| Contact name |
Hanna Najgebauer |
| E-mail(s) |
hanna.najgebauer@gmail.com
|
| Organization name |
University of Liverpool
|
| Department |
Cellular and Molecular Physiology
|
| Street address |
Crown Street
|
| City |
Liverpool |
| ZIP/Postal code |
L69 3BX |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL13534 |
| Series (1) |
| GSE97686 |
Genome-Wide DNA Methylation Profiling of Gastric Cancer-Associated Myofibroblasts |
|
