|
| Status |
Public on Nov 04, 2021 |
| Title |
PS2 |
| Sample type |
SRA |
| |
|
| Source name |
swine testicular cells
|
| Organism |
Sus scrofa |
| Characteristics |
cell type: swine testicular cells
treatment: infected by PDCoV
pdcov strain: PDCoV-CH-HA3-2017 (MK040455)
|
| Treatment protocol |
ST cells were uninfected or infected with PDCoV at a multiplicity of infection (MOI) of 10 and harvested at 11 hour post infection or without, respectively.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from uninfected or infected ST cells using SuPerfecTRITM Total RNA Isolation Reagent (Pufei) according to the manufacturer.
A total amount of 5 µg RNA per sample was used as input material for RNA sample preparation. Firstly, ribosomal RNAs were depleted by using Epicentre Ribo-zero™ rRNA Removal Kit (Epicentre, USA) to get rRNA-depleted RNAs. rRNA-depleted RNAs were further treated with RNase R (Epicentre, USA) and then were subjected to Trizol extraction. Subsequently, sequencing libraries were generated using the rRNA-depleted and RNase R digested RNAs by NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
| |
|
| Description |
Infected at MOI=10 and harvested at 11 hour post infection.
processed data file: novel_circRNA_TPM.xls
|
| Data processing |
Poly-N, adapter and low-quality were removed by in-house perl scripts. Quality control analysis was performed by ng_qc.
Clean reads were aligned to the Sus scrofa Ensembl 76 using Tophat v2.0.9 with the following configurations two passMode Basic --hhlibraryhtypecfrhfirststrand.
circRNAs were identified using find-circ and CIRI as a supplement. The back-spliced reads with at least two supporting reads were annotated as circRNAs.
Expression level of circRNAs was normalized by TPM (transcript per million) through the following criteria: Normalized expression = (mapped reads) / (total reads) * 1000000.
Genome_build: Sus scrofa Ensembl 76
Supplementary_files_format_and_content: novel_circRNA_TPM.xls: Excel file includes normalized values for each Sample.
Supplementary_files_format_and_content: novel_circRNA_gtf.txt
Supplementary_files_format_and_content: novel_circRNA_seq_merged.fa.txt
|
| |
|
| Submission date |
Mar 18, 2020 |
| Last update date |
Nov 04, 2021 |
| Contact name |
LIUYANG Du |
| E-mail(s) |
dlyang57@126.com
|
| Phone |
+8615905193516
|
| Organization name |
Nanjing Agricultural University
|
| Department |
College of Veterinary Medicine
|
| Street address |
WEIGANG NO.1
|
| City |
NANJING |
| State/province |
JIANGSU |
| ZIP/Postal code |
210095 |
| Country |
China |
| |
|
| Platform ID |
GPL22918 |
| Series (1) |
| GSE147188 |
Expression profiles of circular RNAs in ST cells uninfected or infected by PDCoV |
|
| Relations |
| BioSample |
SAMN14400340 |
| SRA |
SRX7950351 |
