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Sample GSM1845297

Query DataSets for GSM1845297

Status

Public on Sep 15, 2016

Title

RNA-Seq zygote_PN5_rep1

Sample type

SRA

Source name

Preimplantation embryo

Organism

Mus musculus

Characteristics

strain: C57BL/6N x PWK
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. Each set of embryos at a particular stage was flushed from the reproductive tract at defined time periods after hCG administration: 20h (MII oocyte), 27-28h (PN5 zygote), 30h (early 2-cell), 43h (late 2-cell), 54-56 h (4-cell), 68-70 h (8-cell) and 92-94 h (blastocysts) in Hepes-buffered CZB medium. The zona pellucida of embryos selected by cell number or morphology was gently removed by treatment of 10 IU/ml pronase (Sigma P8811) for several minutes. The embryos were then manually picked and treated with the lysis buffer for STAR ChIP-seq or Smart-seq2.

Extracted molecule

polyA RNA

Extraction protocol

After removing the zona pellucida, embryonic cells were washed with PBS and incubated in lysis buffer.
RNA-Seq libraries were prepared using Smart-Seq2 protocol with slightly modification

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina HiSeq 1500

Description

processed data file: FPKM_stage.txt.gz

Data processing

Basecalls performed using CASAVA version 1.8
ChIP-seq reads were aligned to the mm9 genome using bowtie 2.2.2, replicates of same stage were pooled together and rpkm in wiggle files were counted by the number of reads falling into 100bp bin in the genome
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 bed files include RPKM values in 100bp bins for each ChIP-seq sample. Bed files labeled maternal or paternal contain RPKM values for two parental alleles, allelic reads were normalized to total reads number. Tab-delimited text files include FPKM values RNA-seq sample.

Submission date

Aug 06, 2015

Last update date

May 15, 2019

Contact name

Bingjie Zhang

Organization name

Tsinghua University

Street address

30 Shuangqing Rd

City

Beijing