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Sample GSM2434095 Query DataSets for GSM2434095
Status Public on Jul 12, 2017
Title Hi-C alpha-amanitin 45h rep2
Sample type SRA
Source name Preimplantation embryo
Organism Mus musculus
Characteristics strain: C57BL/6N x PWK/PhJ
developmental stage: preimplantation embryo
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. PN3 zygotes were treated with 100ug/ml alpha-amanitin for 45h.
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 OTHER
Library source genomic
Library selection other
Instrument model HiSeq X Ten
Data processing Library strategy: HiC-seq
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 Dec 20, 2016
Last update date May 15, 2019
Contact name Zhenhai Du
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
BioSample SAMN06168117
SRA SRX2437879

Supplementary file Size Download File type/resource
GSM2434095_alpha_amanitin_45h_rep2_allValidPairs.txt.gz 652.2 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data are available in SRA

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