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Sample GSM5918855 Query DataSets for GSM5918855
Status Public on Jul 25, 2022
Title FSF1_9
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: 30.46565441
days_in_culture: 31
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 0.760432513046397
cg00000103
cg00000109 0.921371045538328
cg00000155 0.950219758575781
cg00000158 0.948986681691208
cg00000165 0.139379183203606
cg00000221 0.911624016860268
cg00000236 0.858181037873561
cg00000289 0.85123653621276
cg00000292 0.648974444994447
cg00000321 0.372074546512905
cg00000363 0.225106651908867
cg00000540 0.658662165606715
cg00000579 0.955001521957287
cg00000596 0.405920575877662
cg00000622 0.0252594601850503
cg00000658 0.849706939601164
cg00000714 0.200216765449837
cg00000721 0.924119381451516
cg00000734 0.0904529970887744

Total number of rows: 865918

Table truncated, full table size 19397 Kbytes.




Supplementary file Size Download File type/resource
GSM5918855_203723190088_R04C01_Grn.idat.gz 7.0 Mb (ftp)(http) IDAT
GSM5918855_203723190088_R04C01_Red.idat.gz 7.2 Mb (ftp)(http) IDAT
Processed data included within Sample table

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