 |
 |
GEO help: Mouse over screen elements for information. |
|
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 Selector |
Raw data are available in SRA |
Processed data are available on Series record |
|
|
|
|
 |