NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM2940109 Query DataSets for GSM2940109
Status Public on Feb 11, 2019
Title DNA methylation_monkey_SPA
Sample type SRA
 
Source name spermatogonia
Organism Macaca mulatta
Characteristics cell type: spermatogonia
Treatment protocol For the gonocyte or spermatogonia, we separated them from the testis tissue of half-year-old rhesus monkeys. Only spermatogonia could be observed in the seminiferous tubules of testis tissue at this age, through hematoxylin-eosin staining and stage-specific antibody staining (PGP9.5). Testis cells were also collected through two step enzyme digestion. The first step used an enzyme solution in DMEM and the second step used an enzyme solution in 0.25% trypsin EDTA, both containing 1mg/ml collagenase, 1mg/ml DNaseⅠand 2.5 mg/ml hyaluronidase (Cat# H3884, Sigma).
Extracted molecule genomic DNA
Extraction protocol The DNA extraction follows Stem-seq protocol
The STEM-seq libraries were generated using the protocol as described previously(Zhang et al., 2018). Briefly, cells were lysed in lysis buffer (10mM Tris-Hcl PH 7.5, 10mM NaCl,0.5% NP-40, protease K (Roche)) for 3h at 55°C and heat-inactivated for 1h at 72°C. Then we added Lamda DNA as a control to calculate bisulfite conversion rate. The DNA mixture was digested by dsDNA fragmentase (NEB) and followed by bisulfite conversion using EpiTect Fast Bisulfite Conversion Kit (Qiagen). Finally, the purified single strand converted DNA is tailed by poly C, followed by extension with a biotinylated poly G containing primer. The extension product is ligated to an adaptor followed by PCR amplification for sequencing library preparation. All libraries were sequenced on Illumina HiSeq XTen according to the manufacturer’s instruction.
TELP
 
Library strategy Bisulfite-Seq
Library source genomic
Library selection RANDOM
Instrument model HiSeq X Ten
 
Data processing Basecalls performed using CASAVA version 1.8
For Hi-C sapples: sisHi-C sequencing reads were mapped, processed and iteratively corrected using HiC-Pro, a pipeline developed by Servant et al. Briefly, the read pairs were mapped to the mm9 reference genome in a two-step approach with bowtie2. Then the invalid read pairs including dangling end, self-circle ligation and duplicates were discarded. The genome was divided into bins of specific length to generate the contact maps. For global detection of contacts, a 100Kb bin size was used and a 40Kb bin size was used for examination of local domain level contacts. The raw contact counts are normalized with iterative correction.
For methylation samples: STEM-seq reads were aligned to the rheMac2 genome using BSseeker2.0.8, and methylation value in bedGraph files were counted by the number of reads falling into 200bp bin in the genome.
For RNA-seq samples: SMART-seq2 reads were aligned to the rheMac2 or mm9 genome assembly using tophat2 version 2.0.11, then replicates were merged together, and transcript abundance (FPKM) were calculated based on Refseq annotation using cufflinks version 2.0.2.
Genome_build: rheMac2, mm9
Supplementary_files_format_and_content: The bedgraph files contains the values counted by the number of reads falling into 200bp bin in the genome. The gene fpkm txt file contains FPKM value for all samples. with number for each bin. While the validpair txt file indicates the paired interaction reads for each sample.
 
Submission date Jan 18, 2018
Last update date Feb 11, 2019
Contact name Wei Xie
E-mail(s) xiewei121@tsinghua.edu.cn
Organization name Tsinghua University
Street address Zhongguancun north street
City Beijing
ZIP/Postal code 100084
Country China
 
Platform ID GPL24522
Series (1)
GSE109344 Reprogramming of meiotic chromatin architecture during primate spermatogenesis
Relations
BioSample SAMN08375227
SRA SRX3591090

Supplementary file Size Download File type/resource
GSM2940109_monkey_spa_mCG.bedgraph.gz 44.4 Mb (ftp)(http) BEDGRAPH
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap