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Sample GSM4138100

Query DataSets for GSM4138100

Status

Public on Dec 18, 2019

Title

PP rep2

Sample type

SRA

Source name

longissimus dorsi muscle

Organism

Sus scrofa

Characteristics

strain: Qinyu Pig
tissue: muscle
age: 178 days old

Growth protocol

Qinyu pigs were feeded at growth curve inflection point (maximum matabolism rate) (178 days old) and plateau phase (395 days old)

Extracted molecule

total RNA

Extraction protocol

Total RNAs are extracted by Trizol (Invitrogen).Only the RNA samples that had RNA Integrity Number (RIN) scores > 8 were used for further sequencing. .
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

The clean data were obtained by removing reads containing adapters, reads containing over 10 % of poly(N), and low-quality reads (>50 % of the bases had Phred quality scores ≤ 10) from the raw data.
All the downstream analyses were based on the high quality clean data. Pig reference genome and gene annotation files were downloaded from NCBI database (Sscrofa11.1, NCBI). Paired-end clean reads were aligned to the reference genome using Tophat package, the parameters were set as default.
Next, we filtered the assembled novel transcripts from the different libraries to obtain putative lncRNAs following the steps in the pipeline as follows. First, we excluded transcripts that shorter than 200 nt in length, containing less than 2 exons, and containing less than three reads. Next, the coding potential of the remaining transcripts was calculated using the Coding Potential Calculator (CPC) and Coding-Non-Coding Index (CNCI). A transcript with a CPC value lower than -1 and a CNCI value lower than 0 was taken to be an lncRNA.
Genome_build: Sscrofa11.1
Supplementary_files_format_and_content: identified lncRNAs and reads count for each Sample. The file lncRNA.fa includes the transcript sequences for all lncRNA MSTRG* IDs.

Submission date

Oct 24, 2019

Last update date

Dec 18, 2019

Contact name

Jia Luo

E-mail(s)

b20161705@swu.edu.cn

Organization name

Southwest University

Street address

tiansheng road