NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM3190939 Query DataSets for GSM3190939
Status Public on Feb 11, 2019
Title HiC_monkey_PAC_rep3
Sample type SRA
 
Source name pachytene spermatocyte
Organism Macaca mulatta
Characteristics tissue: testes
Treatment protocol Testes in each adult animal were harvested via standard surgical procedure and immediately placed into DMEM medium. After removing laminae parietalis, the testicular tissues were placed in 10 ml dish with DMEM/F12 (Cat# 11330033, Life technology) and cut surgical scissors into 1~2 mm3. Small pieces were washed twice in DMEM/F12 to remove blood cell contaimination and further minced through successive cutting. Frist digestion were incubated for 15 min with a DMEM solution (Cat# 11965-084, Life technology) containing 2mg/ml Collagenase IV (Cat# C5138, Sigma) and 2mg/ml DNaseⅠ(Cat# DN25, Sigma). After spinning down at 600g, the pellet was then incubated with second enzyme digestion containing 2mg/ml collagenase, 2mg/ml DNaseⅠ and 0.25% trypsin EDTA (Cat# 25200-114, Life technology) for approximately 15 min. Digestion were stopped by 10% Fetal Bovine Serum (Cat# 10099-141, Life technology) and the cell suspension were filtered through 100μm and 40μm Strainers (Cat# 352340, BD)
Extracted molecule genomic DNA
Extraction protocol STA-PUT velocity sedimentation cell separator (Chamber Cat#56700-012, ProScience INC, Canada) was applied to generate separation of suspensions of living spematogenic cells on the basis of differences in cell sedimentation rate through the gravity, followed the methods developed for mouse testis cells (Bryant et al., 2013) and the manual of STA-PUT (2010 edition, ProScience INC) . For adult monkeys(5Y), 2-5×107cell/ml testis cell suspension in 1600ml was used with 3hr sedimentation. For neonate monkeys (0.5Y), 600 ml cell suspension was used with 1.5hr sedimentation. According to the visible sedimentation bands, cell suspension was gradually collected through an automatic collector (Cat#DBS-160F, Jinke, China) after velocity sedimentation. All steps for separation were performed at 4°C.And the DNA extraction follows Hi-C protocol.
Hi-C libraries were prepared using Hi-C protocal developed by Rao et al. with slightly modification
 
Library strategy Hi-C
Library source genomic
Library selection other
Instrument model HiSeq X Ten
 
Description monkey_pac_allValidPairs.gz
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 rpkm 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 Jun 14, 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 SAMN09427370
SRA SRX4218883

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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