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Sample GSM5919044 Query DataSets for GSM5919044
Status Public on Jul 25, 2022
Title AVSMC1_GACtl_3
Sample type genomic
 
Source name Iliac vein
Organism Homo sapiens
Characteristics subexperiment: Growth arrest: MMC
coriell_id: AG11546
cell_line: Adult_vascular_smooth_muscle_cell_1
donor_age: 19 years
donor_sex: male
culture_oxygen: Ambient
culture_agent: control
culture_pctfbs: Full
expression_vector: NA
subculture: 2
population_doublings: 32.57816653
days_in_culture: 18
batch_date: 02.20.20
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.
treatment protocol: Primary cells were reintroduced into culture from cryopreserved early-passage cells. Duplicate vehicle subcultures were derived from the initial recovered plate. Vehicle DMSO was added to media and incubated for 3 hours at 37°C before media containing vehicle was removed, cells rinsed with PBS, and basal media replaced. Cells were passaged normally.
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 0.215707805206942
cg00000103
cg00000109 0.66083896940407
cg00000155 0.955075713248918
cg00000158 0.954130857935079
cg00000165 0.56024467591503
cg00000221 0.896397229332021
cg00000236 0.940081812295881
cg00000289 0.882719693050833
cg00000292 0.576890331127781
cg00000321 0.151059975405647
cg00000363 0.501475570754732
cg00000540 0.648899860508267
cg00000579 0.952560318838057
cg00000596 0.278967072588398
cg00000622 0.0182489467265077
cg00000658 0.839981061291941
cg00000714 0.154464302287175
cg00000721 0.937355046953324
cg00000734 0.128292058306423

Total number of rows: 865918

Table truncated, full table size 22664 Kbytes.




Supplementary file Size Download File type/resource
GSM5919044_204088020026_R03C01_Grn.idat.gz 6.9 Mb (ftp)(http) IDAT
GSM5919044_204088020026_R03C01_Red.idat.gz 7.1 Mb (ftp)(http) IDAT
Processed data included within Sample table

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