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Sample GSM5918852 Query DataSets for GSM5918852
Status Public on Jul 25, 2022
Title FSF1_6
Sample type genomic
 
Source name Skin, sacrum
Organism Homo sapiens
Characteristics subexperiment: Baseline profiling
coriell_id: AG06561
cell_line: Fetal_skin_fibroblast_1
donor_age: 16 fetal weeks
donor_sex: female
culture_oxygen: Ambient
culture_agent: NA
culture_pctfbs: Full
expression_vector: NA
subculture: c
population_doublings: 27.6761278
days_in_culture: 26
batch_date: 10.04.19
growth protocol: Fibroblasts were maintained in Eagle’s MEM with Earle’s salts and non-essential amino acids with 15% 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 0.732152479623879
cg00000103
cg00000109 0.914777290974281
cg00000155 0.946946904202301
cg00000158 0.955981884525418
cg00000165 0.161045447375234
cg00000221 0.90796123031346
cg00000236 0.865652958739384
cg00000289 0.84984650944198
cg00000292 0.657946426542165
cg00000321 0.363555005416463
cg00000363 0.222394303411049
cg00000540 0.656768607971405
cg00000579 0.952813503916607
cg00000596 0.398887573954453
cg00000622 0.0241439346683609
cg00000658 0.846111437121024
cg00000714 0.186290718600845
cg00000721 0.929208362615172
cg00000734 0.1138355030802

Total number of rows: 865918

Table truncated, full table size 19406 Kbytes.




Supplementary file Size Download File type/resource
GSM5918852_203723190088_R03C01_Grn.idat.gz 7.0 Mb (ftp)(http) IDAT
GSM5918852_203723190088_R03C01_Red.idat.gz 7.2 Mb (ftp)(http) IDAT
Processed data included within Sample table

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