|
| Status |
Public on Jul 25, 2022 |
| Title |
NFF2_4 |
| 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: b
population_doublings: 14.29362305
days_in_culture: 8
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 |
|
