|
| Status |
Public on Apr 20, 2021 |
| Title |
RNA sequencing Left-Ventricle-1 biological replicate 1 |
| Sample type |
SRA |
| |
|
| Source name |
Left Ventricle
|
| Organism |
Sus scrofa |
| Characteristics |
breed: Rongchang pig
tissue: Left Ventricle
age: 2-year-old
developmental stage: Adult
Sex: female
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using the RNeasy Mini Kit (Qiagen).
We used an rRNA depletion protocol (Ribo-Zero kit, Epicentre) coupled with the Illumina TruSeq stranded RNA-Seq library protocol to construct the RNA-Seq libraries. All libraries were quantified using the Qubit dsDNA High Sensitivity Assay Kit (Invitrogen) and sequenced on HiSeq X Ten (Illumina) platform to produce average ~ 49 million 150-bp paired-end raw reads and ~ 48 million high-quality reads for each library.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
| |
|
| Description |
pig_PCG.all_exp_tpm_gene.txt
pig_lncRNA.all_exp_tpm_gene.txt
pig_TUCP.all_exp_tpm_gene.txt
pig_circRNA.all_exp_tpm_gene.txt
analysis.gtf
Pig-Left-Ventricle-1
|
| Data processing |
Sequence reads are aligned to pig reference genome (Sscrofa 11.1, GCA_000003025.6) by alignment tool STAR (version 2.5.3a).
The aligned reads of these samples were assembled using Cufflinks (version 2.1.1).
We developed and employed a previously reported computational methods to filter out library-specific background noise and predict the most likely isoforms from the assemblies of transcript fragments (transfrags).
After these filtering, we got high-quality assemblies containing reliable transcripts. These high-quality transcript assemblies were then subjected to TACO (a meta-assembly method with a robust solution for leveraging the vast RNA-seq data landscape for transcript structure prediction), leading to the construction of transcriptome maps.
We predicted coding potential by integrating two sources of evidence: (i) predictions from the alignment-free Coding Potential Calculator (CPC2)
LncRNAs were classified into locus biotypes based on both transcription localization and transcription direction of proximal PCG loci (5-kb distance cutoff) with FEElnc software
CIRCExplorer was used to retrieve RNA-seq reads that are mapped to back-splicing junction sites for circRNA prediction
Genome_build: Sscrofa11.1
Supplementary_files_format_and_content: PCG expression level (TPM) text file
Supplementary_files_format_and_content: lncRNA expression level (TPM) text file
Supplementary_files_format_and_content: TUCP expression level (TPM) text file
Supplementary_files_format_and_content: circRNA expression level (TPM) text file
Supplementary_files_format_and_content: gtf file
|
| |
|
| Submission date |
Nov 25, 2020 |
| Last update date |
Apr 20, 2021 |
| Contact name |
jin long |
| E-mail(s) |
longjin8806@163.com
|
| Organization name |
Sichuan Agricultural University
|
| Street address |
Hui ming
|
| City |
Chengdu |
| ZIP/Postal code |
611130 |
| Country |
China |
| |
|
| Platform ID |
GPL22918 |
| Series (2) |
| GSE162145 |
A Pig BodyMap Transcriptome Reveals Diverse Tissue Physiologies and Evolutionary Dynamics of Transcription [RNA-Seq pig] |
| GSE162148 |
A Pig BodyMap Transcriptome Reveals Diverse Tissue Physiologies and Evolutionary Dynamics of Transcription |
|
| Relations |
| BioSample |
SAMN15150275 |
| SRA |
SRX8483887 |
