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Sample GSM4152201

Query DataSets for GSM4152201

Status

Public on Jun 23, 2020

Title

Hi-C_PPN1_rep2

Sample type

SRA

Source name

PPN1 SCNT embryos

Organism

Mus musculus

Characteristics

cell type: SCNT PPN1

Treatment protocol

PPN1 SCNT embryos are collected 4 hours after activation. MII oocytes were obtain at 13-14hrs after hCG injection. The spindle of oocyte was removed by the Piezo-driven (PrimeTech, Osaka, Japan) enucleation pipette on the Olympus inverted microscope (Tokyo, Japan), and the nuclei of donor cells were directly injected into the enucleated oocytes. The reconstructed oocytes were incubated in CZB medium for 1 hour before activation treatment. The cloned constructs were activated in Ca2+-free CZB medium supplemented with 10 mM SrCl2 (Sigma, Cat # 255521) and 5 μg/ml of cytochalasin B (Sigma, Cat # C-6762) for 4 hours. Cloned embryos were cultured in G1-Plus medium (Vitrolife, Cat # 10132) at 37.5 °C in an atmosphere of 5% CO2 in air. The first polar body was removed by enucleation pipette on the micromanipulator, while the zona pellucida was gently removed by treatment with acid Tyrode’s solution (Sigma, Cat # T-1788) for several minutes.

Extracted molecule

genomic DNA

Extraction protocol

The DNA extraction follows Hi-C protocol
Hi-C libraries were prepared using Hi-C protocal developed by Rao et al. with slightly modification
TruSeq

Library strategy

Hi-C

Library source

genomic

Library selection

other

Instrument model

HiSeq X Ten

Description

PPN1_rep12_allValidPairs.txt.gz

Data processing

Basecalls performed using CASAVA version 1.8
For Hi-C samples: 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 and 300Kb bin size wereused and a 40Kb bin size was used for examination of local domain level contacts. The raw contact counts are normalized with iterative correction.
For RNA-seq samples: SMART-seq2 reads were aligned to the mm9 genome assembly using tophat2 version 2.1.1, 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 gene rpkm txt file contains FPKM value for all samples. While the validpair txt file indicates the paired interaction reads for each sample.

Submission date

Nov 06, 2019

Last update date

Jun 23, 2020

Contact name

Ke Zhang

E-mail(s)

zhangke16@mails.tsinghua.edu.cn

Organization name

Tsinghua university

Department

School of Life Sciences