|
| Status |
Public on Jul 25, 2022 |
| Title |
FSF1_SW_15_3 |
| Sample type |
genomic |
| |
|
| Source name |
Skin, sacrum
|
| Organism |
Homo sapiens |
| Characteristics |
subexperiment: Growth arrest: Serum withdrawal
coriell_id: AG06561
cell_line: Fetal_skin_fibroblast_1
donor_age: 16 fetal weeks
donor_sex: female
culture_oxygen: Ambient
culture_agent: NA
culture_pctfbs: 15%
expression_vector: NA
subculture: b
population_doublings: 23.48999471
days_in_culture: 19
batch_date: 02.20.20
growth protocol: Primary fibroblasts were reintroduced into culture from cryopreserved early-passage cells. Fibroblasts were maintained in Eagle’s MEM with Earle’s salts and non-essential amino acids with 15% v/v fetal bovine serum. Triplicate cultures derived from the same parent plate were maintained in parallel. 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 |
|
