|
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).
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|
|
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
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|
|
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 |