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Sample GSM5918902 Query DataSets for GSM5918902
Status Public on Jul 25, 2022
Title AVEC1_26
Sample type genomic
 
Source name Iliac vein
Organism Homo sapiens
Characteristics subexperiment: Baseline profiling
coriell_id: AG11182
cell_line: Adult_vascular_endothelial_cell_1
donor_age: 15 years
donor_sex: male
culture_oxygen: Ambient
culture_agent: NA
culture_pctfbs: Full
expression_vector: NA
subculture: c
population_doublings: 39.88067249
days_in_culture: 74
batch_date: 05.08.19
growth protocol: Vascular endothelial cells were maintained in Medium 199 with 1X GlutaMAX, 0.02mg/ml endothelial cell growth supplement, 0.05 mg/ml sodium heparin, and 15% v/v fetal bovine serum on plates pre-coated with gelatin. 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 0.159240115161358
cg00000103
cg00000109 0.949358203907099
cg00000155 0.958028966697958
cg00000158 0.961753839103304
cg00000165 0.0883546357993455
cg00000221 0.941001190009962
cg00000236 0.94948120856796
cg00000289 0.897880117152254
cg00000292 0.955822921216795
cg00000321 0.55742881035591
cg00000363 0.0943798386120949
cg00000540 0.953603156561428
cg00000579 0.605748664817399
cg00000596 0.0549234187338915
cg00000622 0.0162336757250325
cg00000658 0.890348248946468
cg00000714 0.104397704739736
cg00000721 0.939151622136657
cg00000734 0.0796174482148055

Total number of rows: 865918

Table truncated, full table size 22739 Kbytes.




Supplementary file Size Download File type/resource
GSM5918902_203030040048_R08C01_Grn.idat.gz 6.9 Mb (ftp)(http) IDAT
GSM5918902_203030040048_R08C01_Red.idat.gz 7.1 Mb (ftp)(http) IDAT
Processed data included within Sample table

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