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Sample GSM5919065 Query DataSets for GSM5919065
Status Public on Jul 25, 2022
Title ASF1_GA_5
Sample type genomic
 
Source name Skin, arm
Organism Homo sapiens
Characteristics subexperiment: Growth arrest: MMC
coriell_id: AG16146
cell_line: Adult_skin_fibroblast_1
donor_age: 31 years
donor_sex: male
culture_oxygen: Ambient
culture_agent: MMC
culture_pctfbs: Full
expression_vector: NA
subculture: 3
population_doublings: 7.902606258
days_in_culture: 18
batch_date: 02.20.20
growth protocol: Fibroblasts were maintained in Eagle’s MEM with Earle’s salts with 10% v/v fetal bovine serum. Triplicate cultures derived from the same parent plate or vial obtained from Coriell were maintained in parallel through replicative senescence, which was defined in this study as drastically slowed growth (inability to reach near-confluence at 14 days after previous passage) or viable fraction of cells falling below 60%. Passaging occurred as cells became approximately 90% confluent.
treatment protocol: Primary cells were reintroduced into culture from cryopreserved early-passage cells. Duplicate growth-arrest subcultures were derived from the initial recovered plate. Cells were treated with D intercalating agent mitomycin C reconstituted in DMSO at a fil concentration of 10ug/ml. Cells were incubated for 3 hours at 37°C before media containing MMC was removed, cells rinsed with PBS, and basal media replaced. Cells were collected on days 18 and 25.
Extracted molecule genomic DNA
Extraction protocol Frozen cell pellets were thawed and lysed using QIAshredder spin columns (Qiagen). Genomic DNA was extracted from each sample using the AllPrep DNA/RNA Mini Kit (Qiagen), then stored at -80°C before analysis.
Label Cy3 and Cy5
Label protocol Cy3 and Cy5
 
Hybridization protocol Bisulfite-converted DNA was amplified, fragmented, and hybridized to Illumina Infinium Human Methylation850k Beadchip using standard Illumina protocol.
Scan protocol Arrays were imaged using BeadArray Reader (Illumina HiSeq2000) using standard recommended Illumina scanner setting
Data processing Raw IDATs were processed with R (v4.1.1) package ‘SeSAMe’ with noob background correction, non-linear dye bias correction, and non-detection masking. P-value threshold was set at 0.1. Probe masking was performed using the standard mask list in SeSAMe, including probes that overlap with SNPs and repeat elements.
 
Submission date Feb 26, 2022
Last update date Jul 28, 2022
Contact name Peter W Laird
E-mail(s) Peter.Laird@vai.org
Organization name Van Andel Institute
Department Epigenetics
Lab Peter W Laird
Street address 333 Bostwick Ave NE
City Grand Rapids
State/province MI
ZIP/Postal code 49503
Country USA
 
Platform ID GPL23976
Series (2)
GSE197512 Cell division drives DNA methylation loss in late-replicating domains in primary human cells [methylation array]
GSE197545 Cell division drives DNA methylation loss in late-replicating domains in primary human cells

Data table header descriptions
ID_REF
VALUE beta

Data table
ID_REF VALUE
cg00000029 0.54436898465428
cg00000103
cg00000109 0.861613889641093
cg00000155 0.954383819518624
cg00000158 0.965730400359738
cg00000165 0.316907699269582
cg00000221 0.924903176895757
cg00000236 0.875040407842295
cg00000289 0.902597651447088
cg00000292 0.58576081618113
cg00000321 0.276957214807268
cg00000363 0.177736658979662
cg00000540 0.585005075689184
cg00000579 0.913175976573559
cg00000596 0.220796165190602
cg00000622 0.0195871142714886
cg00000658 0.848760089790456
cg00000714 0.140548902936645
cg00000721 0.947033600899858
cg00000734 0.114854920181554

Total number of rows: 865918

Table truncated, full table size 22608 Kbytes.




Supplementary file Size Download File type/resource
GSM5919065_204088040012_R08C01_Grn.idat.gz 6.9 Mb (ftp)(http) IDAT
GSM5919065_204088040012_R08C01_Red.idat.gz 7.1 Mb (ftp)(http) IDAT
Processed data included within Sample table

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