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Sample GSM7078010 Query DataSets for GSM7078010
Status Public on Apr 20, 2024
Title B6_Ly49DnHp_WGBS
Sample type SRA
 
Source name Spleen
Organism Mus musculus
Characteristics strain: CB6F1/J
tissue: Spleen
cell type: Natural killer cells
subset: Ly49D-H+
genotype: WT
treatment: ex vivo
marker: singlet CD4-CD8-TCRBeta-CD19-NK1.1+NKp46+CD49a-CD49b+
Treatment protocol Splenic NK cells were FACS-sorted from mice
Extracted molecule genomic DNA
Extraction protocol Genome DNA was extracted using Quick-DNA Microprep Kit (Zymo Research, R3020).
WGBS: DNA was sheared to produce 350 bp DNA fragments. 100 ng of DNA fragments were then bisulfite converted using EZ DNA Methylation-Gold Kit (Zymo, D5005) for subsequent WGBS library construction, with xGen Methyl-Seq DNA Library Prep Kit (IDT, 10009860). Amplicon bisulfite: 500ng of genomic DNA was bisulfite-converted using EZ DNA Methylation-Gold Kit (Zymo Research, D5005). The bisulfite-converted DNA was then amplified with target-specific primers using ZymoTaq PreMix (Zymo Research, E2003). Amplicon libraries were then generated using NEBNext Ultra II DNA Library Prep Kit (NEB, E7645).
 
Library strategy Bisulfite-Seq
Library source genomic
Library selection RANDOM
Instrument model Illumina NovaSeq 6000
 
Description singlet CD4-CD8-TCRβ-CD19-NK1.1+NKp46+CD49a-CD49b+
Data processing samples were processed using a custom pipeline publicly available at https://github.com/ChangxuFan/wgbs/tree/fanc
Briefly: trimgalore was used to remove adaptors and low-quality bases; trimmed reads were aligned to the lambda genome using Bismark to assess bisulfite conversion rates. All libraries have > 99.5% conversion rates; trimmed reads were then aligned to the mm10 genome using Bismark, which also calculates the coverage and methylation level of each CpG across the genome; A custom script was used to convert Bismark outputs to methylC tracks, which were visualized using WashU Epigenome Browser.
Amplicon data were processed similar to WGBS. The percentage of reads with a given number of protected cytosines were counted using GenomicAlignments::stackStringsFromBam() in R.
Assembly: mm10
Supplementary files format and content: methylC.gz: methylC tracks for the visualization of the methylation level and sequencing depth at each CpG across the genome
Supplementary files format and content: csv: columns: each CpG covered by the amplicon-based bisulfite sequencing; rows: reads; entries: nucleotide
 
Submission date Mar 02, 2023
Last update date Apr 20, 2024
Contact name Changxu Fan
E-mail(s) fanc@wustl.edu
Organization name Washington University in St. Louis
Department Genetics
Lab Ting Wang Lab
Street address 4515 McKinley Avenue, Room 5213
City Saint Louis
State/province Missouri
ZIP/Postal code 63110
Country USA
 
Platform ID GPL24247
Series (2)
GSE226500 Epigenetic evolution of the Ly49 gene family [Bisulfite-Seq]
GSE226502 Epigenetic evolution of the Ly49 gene family
Relations
BioSample SAMN33569408
SRA SRX19549716

Supplementary file Size Download File type/resource
GSM7078010_B6_Ly49DnHp_WGBS_CpG.methylC.txt.gz 168.8 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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