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Sample GSM5918933 Query DataSets for GSM5918933
Status Public on Jul 25, 2022
Title ASF1_7
Sample type genomic
 
Source name Skin, arm
Organism Homo sapiens
Characteristics subexperiment: Baseline profiling
coriell_id: AG16146
cell_line: Adult_skin_fibroblast_1
donor_age: 31 years
donor_sex: male
culture_oxygen: Ambient
culture_agent: NA
culture_pctfbs: Full
expression_vector: NA
subculture: c
population_doublings: 21.36307631
days_in_culture: 50
batch_date: 12.26.18
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.
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 0.701004067488184
cg00000103
cg00000109 0.943427341188527
cg00000155 0.958751544910805
cg00000158 0.96909956711046
cg00000165 0.161673833450133
cg00000221 0.916530782292045
cg00000236 0.950030485222973
cg00000289 0.909164916920693
cg00000292 0.601293954262355
cg00000321 0.185888678504156
cg00000363 0.162720709431553
cg00000540 0.396414678948581
cg00000579 0.91834585691624
cg00000596 0.0792557723649413
cg00000622 0.0170026547202296
cg00000658 0.850477570096954
cg00000714 0.214952934777035
cg00000721 0.960529853508041
cg00000734 0.105659663889737

Total number of rows: 865918

Table truncated, full table size 22775 Kbytes.




Supplementary file Size Download File type/resource
GSM5918933_202253620097_R04C01_Grn.idat.gz 7.0 Mb (ftp)(http) IDAT
GSM5918933_202253620097_R04C01_Red.idat.gz 7.2 Mb (ftp)(http) IDAT
Processed data included within Sample table

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