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Sample GSM5919028 Query DataSets for GSM5919028
Status Public on Jul 25, 2022
Title NFF2_40
Sample type genomic
 
Source name Foreskin
Organism Homo sapiens
Characteristics subexperiment: Baseline profiling
coriell_id: AG21859
cell_line: Neonatal_foreskin_fibroblast_2
donor_age: 0 years
donor_sex: male
culture_oxygen: Ambient
culture_agent: NA
culture_pctfbs: Full
expression_vector: NA
subculture: c
population_doublings: 55.88728255
days_in_culture: 72
batch_date: 08.31.18
growth protocol: Fibroblasts were maintained in Ham’s F12/DMEM 1:1 media supplemented 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 0.287328858106624
cg00000103
cg00000109 0.910000657688708
cg00000155 0.950951301022324
cg00000158 0.940956243725829
cg00000165 0.123397498516485
cg00000221 0.89182301696515
cg00000236 0.89516701934738
cg00000289
cg00000292 0.706976945566402
cg00000321 0.162538731271238
cg00000363 0.114865913916824
cg00000540 0.56120043743747
cg00000579 0.828502085068661
cg00000596 0.279277803333528
cg00000622 0.0206403009368993
cg00000658 0.867420527251386
cg00000714 0.166612986971436
cg00000721 0.749378588912351
cg00000734 0.107014807278389

Total number of rows: 865918

Table truncated, full table size 22140 Kbytes.




Supplementary file Size Download File type/resource
GSM5919028_202253660120_R07C01_Grn.idat.gz 7.0 Mb (ftp)(http) IDAT
GSM5919028_202253660120_R07C01_Red.idat.gz 7.2 Mb (ftp)(http) IDAT
Processed data included within Sample table

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