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Sample GSM3516925

Query DataSets for GSM3516925

Status

Public on Dec 17, 2019

Title

day_0 rep1

Sample type

SRA

Source name

Whole-blood tissue

Organism

Sus scrofa

Characteristics

development stage: newborn
tissue: Whole-blood
age: 0 days after birth

Extracted molecule

total RNA

Extraction protocol

Total RNA was isolated from each sample with Trizol reagent (Life Technologies, Beijing, China) according to the manufacturer's instruction.
Approximately 1 µg total RNA and the Ribo-Zero™ kit (Epicentre, Madison, WI, USA) were used to generate RNA-Seq cDNA libraries from each sample, and then, RNA sequencing was performed following the manufacturer's standard procedures.

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

HiSeq X Ten

Description

domestic pig
D0_1

Data processing

Illumina CASAVA ver.1.8.2 software was used for basecalling.
We removed low-quality reads including those with ≥ 10% unidentified nucleotides, > 10 nt aligned to the adapter, allowing ≤ 10% mismatches, and with > 50% of bases with phred quality < 5. Then, high-quality reads of ten strand-specific libraries were mapped to the pig reference genome (Suscrofa.11.1 from Ensemble) with Hisat2 (v.2.0.4)
mRNA expression levels of fragments per kilobase per million mapped reads (FPKM) were obtained using Stringtie (v.1.3.3).
Transcripts were assembled by Stringtie version 1.3.3.
Cuffmerge (part of Cufflinks, version 2.2.1) was used to merge the assembled transcripts.
Coffcompare (part of Cufflinks, version 2.2.1) was used to remove transcripts annotated in the reference sequence (marked by ‘c’ for partial match or ‘=’ for full match).
Each transcript sequence was translated in all six possible frames with Transeq (part of EMBOSS version 6.5.7) and the transcript with translated protein sequences that had a significant hit in the Pfam (release27) database with HMMER (v3.1b2) were excluded.
Remaining transcripts were compared with human and mouse genomes, and the UniRef database with BLASTX, then, potential coding transcripts were removed.
The Coding Potential Calculator (CPC) was used to assess the coding potential of the remaining transcripts.
Genome_build: Suscrofa.11.1 from Ensemble
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each sample.

Submission date

Dec 17, 2018

Last update date

Dec 17, 2019

Contact name

Zhou rui

E-mail(s)

zhourui0122@foxmail.com

Phone

18080182910

Organization name

Sichuan Agricultural University