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Sample GSM491351 Query DataSets for GSM491351
Status Public on Dec 29, 2009
Title Newborn Human Foreskin Fibroblasts: Bisulfite sequencing
Sample type SRA
Source name Primary fibroblast
Organism Homo sapiens
Characteristics cell type: Newborn Human Foreskin Fibroblasts
Growth protocol WA09 hESC line was cultured feeder-free on MatrigelTM (Becton-Dickinson) in StemPro TM medium (Lifetech, Inc.), and passaged with Accutase (Lifetech, Inc.). They were harvested at passage 41. hESC-derived fibroblasts (hESC-Fibro) were derived as a stable proliferating population from spontaneously differentiating passage 40 WA09 hESC cells (Gonzalez et al., 2008); after their differentiation they were expanded in two batches, to passage 11 and passage 13 before harvesting. The neonatal fibroblast line (Fibro) cell line was obtained from GlobalStem, Inc (catalog number GSC-3002, Newborn Human Foreskin Fibroblasts, untreated) and was harvested for analysis at passage 13. All cell lines were cultured at 37°C, ambient oxygen, and 5% CO2. The hESC-Fibro and Fibro cell lines were cultured in DMEM+10%FBS and passaged with trypsin.
Extracted molecule genomic DNA
Extraction protocol Genomic DNA were extracted from the individual cell lines and fragmented via nebulization to sizes between 300 bp to 500 bp. The fragmented DNA was end polished and ligated with Illumina methylated PE adaptors followed by two consecutive bisulfite treatments using the EpiTect Bisulfite Kit (Qiagen) to ensure maximal conversion rate. The bisulfite treated DNA was enriched by 10 cycles of PCR with primers complementary to the adaptor sequences by uracil-insensitive Taq polymerase (Pfu Turbo Cx Hotstart DNA Polymerase; Stratagene). Sizes between 250 bp to 300 bp (including the adaptors) were selected and sequenced with the Illumina Genome Analyzer using the PE sequencing method at 75bp read length
Library strategy OTHER
Library source genomic
Library selection other
Instrument model Illumina Genome Analyzer II
Description Fibro DNA methylation mapping data
Data processing Alignment: Sequence reads were first processed by Illumina Genome Analyzer pipeline for base calling and quality filtering. Reads that passed filtering were aligned to human reference genome, Hg18, via SOAP2 alignment program with less than 2 mismatches. To accommodate the conversion of unmethylated cytosines to thymines by bisulfite conversion, we used a "reduced", three-letter alphabet comprising A, G and {C or T} to represent the genome.
Methylation levels of a C within an aligned read were gauged by the ratio of reads that contained a methylated C at that location vs. all the reads that covered the location.
Submission date Dec 28, 2009
Last update date May 15, 2019
Contact name Chia-Lin Wei
Phone 65 64788074
Fax 65 64789059
Organization name Genome Institute of Singapore
Department Genome Technology & Biology
Street address 60 Biopolis Street #02-01
City Singapore
ZIP/Postal code 138672
Country Singapore
Platform ID GPL9115
Series (1)
GSE19418 Dynamic Changes in the Human Methylome During Differentiation
Reanalyzed by GSE46644
SRA SRX015769
SRA SRX015770
SRA SRX015771
SRA SRX015772
BioSample SAMN00007499

Supplementary data files not provided
SRA Run SelectorHelp
Processed data are available on Series record
Raw data are available in SRA

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