|
Status |
Public on Jul 25, 2022 |
Title |
FSF1_SW_05_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: 0.50% expression_vector: NA subculture: c population_doublings: 20.43311181 days_in_culture: 36 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 0.5% 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.
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|
|
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 |
|