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Sample GSM4988100 Query DataSets for GSM4988100
Status Public on Dec 24, 2023
Title genomic DNA from fibroblasts from donor 911VI
Sample type genomic
 
Source name donor 911VI
Organism Homo sapiens
Characteristics donor: 911VI
disease: Healthy
diagnosis: Healthy
mutation: Wild type (WT)
group: NonAGED
csa/csb: NA
Sex: Male
age at skin biopsy (yrs): NA
age at death or latest report (yrs): NA
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 911VI, Healthy, Wild type (WT)
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

Supplementary file Size Download File type/resource
GSM4988100_200400320115_R01C01_Grn.idat.gz 4.0 Mb (ftp)(http) IDAT
GSM4988100_200400320115_R01C01_Red.idat.gz 4.1 Mb (ftp)(http) IDAT
Processed data are available on Series record

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