|
| Status |
Public on Jun 09, 2023 |
| Title |
WGBS_029_O4_luminal |
| Sample type |
SRA |
| |
|
| Source name |
Mammary luminal epithelial cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Mammary luminal epithelial cells
age: 68 y
facs sort group: CD133+/CD271-
|
| Growth protocol |
Cells were grown in M87A medium with cholera toxin and oxytocin at 0.5 ng/ml and 0.1nM, respectively. Cells were stained with anti-human CD133-PE (Biolegend, clone 7) and anti-human CD271 (Biolegend, clone ME20.4) by following standard flow cytometry protocol. Luminal epithelial cells were enriched with Aria III (Becton Dickinson) as CD133+/CD271- fractions.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Quick-DNA Microprep kit (Zymo Research) was used to extract DNA.
Genomic DNA was bisulfite converted using the Zymo EZ DNA methylation kit (Zymo Research). Library preparation was done using TruSeq DNA Methylation Kit with 75ng of bisulfite converted DNA as per manufacturer’s recommendations.
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Raw sequencing reads were adapter trimmed and hard trimmed 8 bp from both ends using Trim Galore v0.4.5.
Trimmed reads were aligned to the human reference genome hg19 using Bismark v0.19.1 with the --bowtie1 option.
PCR duplicates were removed using Bismark. Methpipe v3.4.3 was used to determine the methylation status of individual CpG sites.
Genome_build: hg19
Supplementary_files_format_and_content: Bed format, columns: chr, CpG site, strand, cytosine context, methylation level (0 to 1), coverage
|
| |
|
| Submission date |
Jul 12, 2021 |
| Last update date |
Jun 09, 2023 |
| Contact name |
Dustin E Schones |
| E-mail(s) |
dschones@coh.org
|
| Organization name |
City of Hope
|
| Street address |
1500 E Duarte Rd.
|
| City |
Duarte |
| State/province |
CA |
| ZIP/Postal code |
91010 |
| Country |
USA |
| |
|
| Platform ID |
GPL24676 |
| Series (2) |
| GSE153309 |
Loss of epigenetic suppression of retrotransposons with oncogenic potential in aging mammary luminal epithelial cells |
| GSE153696 |
Age associated epigenome changes in human mammary epithelial cells |
|
| Relations |
| BioSample |
SAMN20170231 |
| SRA |
SRX11411286 |
