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Sample GSM4086443 Query DataSets for GSM4086443
Status Public on Jul 17, 2020
Title PS_bisulfite-seq
Sample type SRA
 
Source name testis
Organism Mus musculus
Characteristics tissue: testis
cell type: pachytene spermatocytes
development stage: 6-8 weeks
strain: C57BL/6
Extracted molecule genomic DNA
Extraction protocol DNA is extracted through Wizard Genomic DNA Purification Kit(LOT 0000139127).
The sequencing libraries were generated using the Pico Methyl-Seq Library Prep Kit (D5456, Zymo Research) following the manufacturer's instructions.
 
Library strategy Bisulfite-Seq
Library source genomic
Library selection RANDOM
Instrument model HiSeq X Ten
 
Description whole genome
ploidy: 4N
Data processing Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, low quality and low complexity reads, then mapped to mm9 reference genome using using bsmap(v 2.89) with parameter “--s 16 -v 0.1 -n 1 -R".
Methylation level of each CpG site was estimated using mcall(v 1.3.0) with default parameters, and output bed format files are transformed to tab-delimited text files using custom python scripts.
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text files include methylation level and coverage for each CpG site.
 
Submission date Sep 19, 2019
Last update date Jul 18, 2020
Contact name liu ying dong
E-mail(s) liuyingdong2017@126.com
Phone 18729187605
Organization name Northwest University of Agriculture and Forestry Science and Technology
Department College of Animal Science and Technology
Lab Zeng wenxian
Street address Shaanxi
City Xi'an, Shaanxi
ZIP/Postal code 710000
Country China
 
Platform ID GPL21273
Series (2)
GSE137743 Whole genome bisulfite Sequencing data of four types mouse spermatogenesis
GSE137744 ltra-low-input native ChIP-seq and Whole genome bisulfite Sequencing data of four types mouse spermatogenesis
Relations
BioSample SAMN12788970
SRA SRX6874360

Supplementary file Size Download File type/resource
GSM4086443_PS.bsmap.CpG.txt.gz 128.8 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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