|
| Status |
Public on Dec 24, 2023 |
| Title |
genomic DNA from fibroblasts from donor CS539VI |
| Sample type |
genomic |
| |
|
| Source name |
donor CS539VI
|
| Organism |
Homo sapiens |
| Characteristics |
donor: CS539VI
disease: Cockayne syndrome (CS)
diagnosis: CS type I
mutation: csb
group: CS
csa/csb: abscence of CSB
Sex: Female
age at skin biopsy (yrs): 3
age at death or latest report (yrs): 8
|
| Growth protocol |
Patient fibroblasts were derived from skin biopsies excised from unexposed body sites by dermatologists. Healthy, UVSS and CS cells initially thawed at passage number (PN) 12 were cultured in Dulbecco's modified eagle medium (DMEM; Gibco) supplemented with 2mM L-glutamine (GlutaMAX™; Gibco), 10% foetal bovine serum (FBS; Gibco), 1% Penicillin-streptomycin (Gibco) in 20% O2/5% CO2 at 37 °C. Cells were harvested at PN14 for further experiments.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Total genomic DNA (gDNA) from WT, UVSS and CS primary skin fibroblasts was isolated using the QIamp® DNA mini kit (Qiagen) and used for microarray-based analysis of genome wide DNA methylation levels in two different sets. For the first set, extracted gDNA was quantified by NanoDrop (ND-1000; Thermo Fisher Scientific) and 1µg was bisulfite-treated using the EZ DNA Methylation™ kit (Zymo Research), according to manufacturer instructions. Genone-wide DNA methylation analysis was performed on this material by Aros Applied Biotechnology A/S (Eurofins Genomics; Denmark) using the Infinium HumanMethylation450 BeadChip (Illumina). For the second set, extracted gDNA was directly send to Aros Applied Biotechnology A/S for bisulfite conversion and genome-wide DNA methylation using the Infinium MethylationEPIC BeadChip (Illumina) following manufacturer's instructions.
|
| Label |
Cy3 and Cy5
|
| Label protocol |
Standard Illumina Protocol
|
| |
|
| Hybridization protocol |
Bisulphite converted DNA was amplified, fragmented and hybridised to Infinium BeadChip using standard Illumina protocol
|
| Scan protocol |
HiScan scanner (Illumina)
|
| Description |
genomic DNA from fibroblasts from donor CS539VI, CS type I, csb
|
| Data processing |
Signal intensities files were extracted using the minfi Bioconductor package. The preprocessNoob function implemented in minfi was applied to normalize raw data.
|
| |
|
| Submission date |
Dec 24, 2020 |
| Last update date |
Dec 24, 2023 |
| Contact name |
Maria Giulia Bacalini |
| E-mail(s) |
mugiu17@hotmail.com
|
| Phone |
00390512094748
|
| Organization name |
IRCCS Istituto delle Scienze Neurologiche di Bologna
|
| Department |
Brain Aging Laboratory
|
| Street address |
Via Altura 3
|
| City |
Bologna |
| ZIP/Postal code |
40139 |
| Country |
Italy |
| |
|
| Platform ID |
GPL13534 |
| Series (2) |
| GSE163839 |
DNA methylation of fibroblasts from Cockayne syndrome and UV-sensitivity syndrome patients [450k] |
| GSE163841 |
DNA methylation of fibroblasts from Cockayne syndrome and UV-sensitivity syndrome patients |
|
