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Sample GSM2828339

Query DataSets for GSM2828339

Status

Public on Nov 01, 2018

Title

SR3

Sample type

SRA

Source name

Spleen

Organism

Sus scrofa

Characteristics

breed: Y x L
age: 7-day old
infection: Clostridium perfringens type C
group: SR
tissue: spleen

Extracted molecule

total RNA

Extraction protocol

Spleen were removed, flash frozen and total RNA was extracted from each sample using TRIzol reagent (Invitrogen, Carlsbad, CA, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina HiSeq 4000

Data processing

Fastq format raw reads (raw data) were handled through in-house perl scripts. Clean reads (clean data) were gained by removing adapters, ploy-N and low quality reads from raw reads (raw data). Meanwhile, Q20, Q30 and GC content of the clean data were evaluated. The paired-end clean reads were mapped to the pig genome sequence assembly (Sscrofa 10.2) with Tophat (v2.0.9) software.
CNCI, CPC, PFAM and phyloCSF, were used to obtain the candidate lncRNA. Firstly, transcripts without coding potential were achieved using any of the four tools with earlier described instructions. Next, those without coding potential shared by four tools were screened as the candidate lncRNAs for subsequent research.
The genes expression level of both lncRNAs and protein-coding in each sample was calculated by FPKM (fragments per kb for a million reads) evaluated using Cuffdiff (v2.1.1)
To explore transcripts conservation, the Phast (v1.3) software was widely used for phylogenetic analysis and thus phastCons expression.
Gene Ontology (GO) enrichment analysis of differentially expressed genes or lncRNA target genes were implemented by the GOseq R package. KOBAS software was performed to test the statistical enrichment of differential expression genes or lncRNA target genes in KEGG pathways.
Coding genes 10k/100k upstream and downstream of lncRNA were treated as the cis target gene. Then, the trans role of lncRNA is to identify using the expression level.
Genome_build: Sus scrofa 10.2
Supplementary_files_format_and_content: Tab-delimited text file includes FPKM values for each Sample

Submission date

Oct 23, 2017

Last update date

May 15, 2019

Contact name

y zun qiang

E-mail(s)

756707388@qq.com

Phone

18719823101

Organization name

College of Animal Science and Technology