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Sample GSM4982859

Query DataSets for GSM4982859

Status

Public on Nov 26, 2021

Title

bovine_FGO_Smartseq_rep2

Sample type

SRA

Source name

oocyte

Organism

Bos taurus

Characteristics

developmental stage: full_grown oocyte

Extracted molecule

polyA RNA

Extraction protocol

RNA library preparation and sequencing The RNA libraries for mammalian oocytes and preimplantation embryos were prepared using Smart-seq2 method as previously reported (Picelli et al., 2014).

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

HiSeq X Ten

Description

cow_RNA_fpkm.txt

Data processing

Basecalls performed using CASAVA version 1.8
All STEM-seq datasets were firstly treated with cutadapt v1.11 (Martin, 2011) and the low-quality reads and adaptors were removed before mapping. Then all filtered reads were aligned to different genomes (rat, rn6; cow, bosTau8; pig, susScr11) using Bismark (v0.7.0；bowtie2 2.1.0) (Krueger and Andrews, 2011) with default parameters. Multi-mapped reads and PCR duplicates were removed also with the Bismark. The unique mapped reads were used for CpG methylation calling with bismark_methylation_extractor. For every single CpG site, only the CpG sites that were covered at least 3 times were used for further analysis. The spiked-in Lamda DNA (1:200) was used for conversation rate calculation.
All RNA-seq datasets were mapped to the different genomes (rat: rn6; cow: bosTau8; pig: susScr11). All genomes were downloaded from UCSC (citation) by Tophat v2.1.1 (Trapnell et al., 2009). Gene expression was then calculated according to refFlat database by cufflinks 2.2.1 (Trapnell et al., 2012).
All reads were firstly processed by TrimGalore (v.0.6.4) with default parameters to remove the poor qualitied reads and also the adapters. Then the filtered reads were mapped to different genomes (rat: Rn6; cow: bosTau8; pig: susScr11) by Bowtie2 (v2.2.5) (Langmead and Salzberg, 2012) with the default parameters. All multiple mapped reads as well as the duplicates were removed with MarkDuplicates.jar. Then all unique mapped reads were used for the downstream RPKM (reads per kilobase per million of sequenced reads) calculation. The Pearson correlation was generated for each sample with two biological replicates with 10 kb bins. The replicates with good reproducibility were pooled for downstream analysis.
Supplementary_files_format_and_content: The cov txt files contains the chr, start positon, methylated CG count, unmethylated CG count. The txt files for FPKM contain gene names and the FPKM value for all stages.

Submission date

Dec 21, 2020

Last update date

Nov 26, 2021

Contact name

Wei Xie

E-mail(s)

xiewei121@tsinghua.edu.cn

Organization name

Tsinghua University

Street address

Zhongguancun north street