|
Status |
Public on Jul 12, 2017 |
Title |
Hi-C alpha-amanitin 45h rep1 |
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 |
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 |
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 |
SAMN06168118 |
SRA |
SRX2437878 |