NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM2700110 Query DataSets for GSM2700110
Status Public on Jul 12, 2017
Title Hi-C PN3 zygote rep2
Sample type SRA
 
Source name Preimplantation embryo
Organism Mus musculus
Characteristics strain: C57BL/6N x PWK/PhJ
developmental stage: PN3 zygote
Treatment protocol Embryos were collected from C57BL/6N mice induced to superovulation by injections of 5 IU of pregnant mare’s serum gonadotrophin(Ningbo Sansheng Pharmaceutical Co, Ltd) and 5 IU of human chorionic gonadotrophin(Ningbo Sansheng Pharmaceutical Co, Ltd) 44-48 hours apart and mated to PWK males.
Extracted molecule genomic DNA
Extraction protocol After removing the zona pellucida, embryonic cells were washed with PBS and fixed with 1% formaldehyde for 10min at RT.
HiC libraries were prepared using sisHi-C similar with in situ Hi-C method developed by Rao et al.
 
Library strategy Hi-C
Library source genomic
Library selection other
Instrument model HiSeq X Ten
 
Description processed data file:
PN3_rep12_allValidPairs.txt.gz, PN3_rep12_maternal_allValidPairs.txt.gz, PN3_rep12_paternal_allValidPairs.txt.gz
Data processing Basecalls performed using CASAVA version 1.8
Hi-C reads are processed using HiCPro version2.7.1b and replicates of same stage were pooled together
Compartment analysis are done as previously described. (Dixon et al., 2015)
TAD calling is done using Insulation score method as previously described ( Crane et al., 2015)
RNA-Seq reads were aligned to the mm9 genome assembly using Tophat 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: mm9
Supplementary_files_format_and_content: The files including all the valid interaction pairs ( described as Servant et al., 2015). The valid pairs are stored using a simple tab-delimited text format ; read name / chr_reads1 / pos_reads1 / strand_reads1 / chr_reads2 / pos_reads2 / strand_reads2 / fragment_size [/ allele_specific_tag]
 
Submission date Jul 11, 2017
Last update date May 15, 2019
Contact name Zhenhai Du
E-mail(s) duzhenhai93220@gmail.com
Organization name Tsinghua University
Street address Qinghua Yuan, Haidian District
City Beijing
ZIP/Postal code 100084
Country China
 
Platform ID GPL21273
Series (1)
GSE82185 Allelic reprogramming of 3D chromatin architecture during early mammalian development
Relations
BioSample SAMN07343012
SRA SRX2996184

Supplementary file Size Download File type/resource
GSM2700110_PN3_rep2_allValidPairs.txt.gz 1.0 Gb (ftp)(http) TXT
GSM2700110_PN3_rep2_maternal_allValidPairs.txt.gz 400.7 Mb (ftp)(http) TXT
GSM2700110_PN3_rep2_paternal_allValidPairs.txt.gz 296.3 Mb (ftp)(http) TXT
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