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Sample GSM5918911 Query DataSets for GSM5918911
Status Public on Jul 25, 2022
Title AVSMC1_4
Sample type genomic
 
Source name Iliac vein
Organism Homo sapiens
Characteristics subexperiment: Baseline profiling
coriell_id: AG11546
cell_line: Adult_vascular_smooth_muscle_cell_1
donor_age: 19 years
donor_sex: male
culture_oxygen: Ambient
culture_agent: NA
culture_pctfbs: Full
expression_vector: NA
subculture: a
population_doublings: 34.30861599
days_in_culture: 20
batch_date: 12.26.18
growth protocol: Vascular smooth muscle cells were maintained in Medium 199 with 1X GlutaMAX, 0.02mg/ml endothelial cell growth supplement, 0.05 mg/ml sodium heparin, and 10% 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 0.124686140137229
cg00000103
cg00000109 0.644171675665016
cg00000155 0.971961644029287
cg00000158 0.979322147607933
cg00000165 0.638205580885154
cg00000221 0.925435487553513
cg00000236 0.970684786580824
cg00000289
cg00000292 0.538769265372117
cg00000321 0.0773579377476807
cg00000363 0.600038065351751
cg00000540 0.675345638572501
cg00000579 0.971099242199695
cg00000596 0.301517785895627
cg00000622 0.0112003509487827
cg00000658 0.867096836221857
cg00000714 0.101055625865342
cg00000721 0.958403193168825
cg00000734 0.0666172905083531

Total number of rows: 865918

Table truncated, full table size 22560 Kbytes.




Supplementary file Size Download File type/resource
GSM5918911_202253620109_R08C01_Grn.idat.gz 7.0 Mb (ftp)(http) IDAT
GSM5918911_202253620109_R08C01_Red.idat.gz 7.2 Mb (ftp)(http) IDAT
Processed data included within Sample table

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