|
| Status |
Public on Jun 19, 2024 |
| Title |
OLD Biological Rep 2, Passage 2 |
| Sample type |
SRA |
| |
|
| Source name |
dermal fibroblasts
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: dermal fibroblasts
age (years): 86
passage: 2
|
| Growth protocol |
All fibroblasts were thawed in passage 2 (P2) and maintained in Human Dermal Fibroblast Media (#116-500, Cell Applications). Media was refreshed every other day and fibroblasts were passaged using Tryple Select (12563011,Gibco) when culture dishes were >80% confluent. Cell pellets were frozen down every passage (P2-P8) to establish a large database of samples.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA from neonatal and old fibroblast cells was extracted using the GeneJET genomic DNA extraction kit (Thermo Scientific, Cat.n.K0721). DNA samples were quantified by Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA).
WGBS library preparation and sequencing reactions were conducted at Novogene Corporation Inc (Sacramento, CA, USA).
Whole Genome Enzymatic Conversion
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
Whole Genome Ezymatic Conversion
ALL_fibropass.hmr.txt
OLD3_allPs.hmr.txt
|
| Data processing |
Trimming (Trimgalore)
Mapping (Bismark)
Conversion to methpipe/DNMTools formatted SAM using DNMTools
Duplicate reads removed, individual CpG coverage/average methylation calculated for symmetrical CpGs, using methpipe. Symmetrical CpG counts were then converted to bigwig format with wigToBigWig function
Low methylated regions (LMRs) calculated from symmetrical CpG counts file using hmr function in methpipe.
Assembly: hg38
Supplementary files format and content: bigwig files containing methylation pecentage per symmetric CpG in UCSC format
Supplementary files format and content: hmr files are genomic coordinates of low methylated regions for either all neonatal passages merged (NEO2_allPs.hmr.txt), all old passages merged (OLD3_allPs.hmr.txt), or all neonatal and old passages merged (ALL_fibropass.hmr.txt).
|
| |
|
| Submission date |
Jan 23, 2024 |
| Last update date |
Jun 19, 2024 |
| Contact name |
Vittorio Sebastiano |
| E-mail(s) |
vsebast@stanford.edu
|
| Organization name |
Stanford University
|
| Department |
OB-GYN/Reproductive, Perinatal and Stem Cell Biology Research
|
| Lab |
Sebastiano Lab
|
| Street address |
265 Campus Drive
|
| City |
Stanford |
| State/province |
California |
| ZIP/Postal code |
94305-5454 |
| Country |
USA |
| |
|
| Platform ID |
GPL24676 |
| Series (2) |
| GSE253985 |
PRC2-AgeIndex: a universal biomarker of aging and rejuvenation [WGBS] |
| GSE253987 |
PRC2-AgeIndex: a universal biomarker of aging and rejuvenation |
|
| Relations |
| BioSample |
SAMN39575485 |
| SRA |
SRX23363337 |
