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Sample GSM5919187 Query DataSets for GSM5919187
Status Public on Jul 25, 2022
Title FSF1_TERT_34
Sample type genomic
 
Source name Skin, sacrum
Organism Homo sapiens
Characteristics subexperiment: TERT immortalization
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: Full
expression_vector: TERT
subculture: 2a
population_doublings: 89.12
days_in_culture: 163
batch_date: 09.24.21
growth protocol: 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 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: Low-PD primary fibroblasts were transduced with purified lentiviral particles containing expression vectors encoding human Telomerase Reverse Transcriptase (TERT) and hygromycin resistance marker. Following selection with 250ug/ml hygromycin B, cells were serially cultured in perpetuity, in triplicate.
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 0.141990451197914
cg00000103
cg00000109 0.879239589539197
cg00000155 0.956348112761032
cg00000158 0.948343671115757
cg00000165 0.196579851464488
cg00000221 0.907216539175177
cg00000236 0.925503154349827
cg00000289
cg00000292 0.52212816769636
cg00000321 0.706373132568327
cg00000363 0.650935605120766
cg00000540 0.539399210392815
cg00000579 0.954860569346505
cg00000596 0.0551590415115146
cg00000622 0.019104959791558
cg00000658 0.890552389312089
cg00000714 0.287301459468564
cg00000721 0.792655676794426
cg00000734 0.088585211263344

Total number of rows: 865918

Table truncated, full table size 22020 Kbytes.




Supplementary file Size Download File type/resource
GSM5919187_205567980156_R07C01_Grn.idat.gz 7.0 Mb (ftp)(http) IDAT
GSM5919187_205567980156_R07C01_Red.idat.gz 7.1 Mb (ftp)(http) IDAT
Processed data included within Sample table

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