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Sample GSM5437063 Query DataSets for GSM5437063
Status Public on Jun 09, 2023
Title WGBS_356E_Y5_luminal
Sample type SRA
 
Source name Mammary luminal epithelial cells
Organism Homo sapiens
Characteristics cell type: Mammary luminal epithelial cells
age: 21 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 SAMN20170228
SRA SRX11411289

Supplementary file Size Download File type/resource
GSM5437063_356E_CpG_meth.bed.gz 158.7 Mb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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