|
| Status |
Public on Jun 01, 2021 |
| Title |
T8.RNA-seq.ML |
| Sample type |
SRA |
| |
|
| Source name |
T8
|
| Organism |
Trichinella sp. T8 |
| Characteristics |
strain: ISS124
passages: Muscle larvae
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA of T. spiralis (Ad, NBL and ML) was purified using Trizol reagent (Invitrogen, CA, USA) according to the manufacturer’s instructions.
To degrade any possible DNA contamination, the total RNA samples were dissolved in diethylpyrocarbonate (DEPC)-treated water and treated with DNaseI. NanoDrop 2000 (Thermo Scientific CA, USA) was then used to assess the quantity and quality of the total mRNA enriched using oligo (dT) magnetic beads. Paired-end sequencing libraries with insert size of 300 bp were conducted on the HiSeq 2,500 platform following the Illumina’s protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
T8
|
| Data processing |
SOAPnuke was used for trimming adapters and filtering on length and quality of the raw sequencing reads, with the following paramaters: -q 0.5 -d -Q 2 --sanger -l 20
Clean reads were mapped to respective reference genome using hisat2 with default settings
The levels of gene expression were quantified using Cufflinks (v2.2.1) with RPKM (reads per kilobase million).
Differentially expressed genes were estimated by Cuffdiff (v2.2.1) with default paramaters
Genes with a threshold false discovery rate (FDR) ≤ 0.05 and the absolute value of log2Ratio ≥ 1 or ≤ -1 were considered significantly differentially expressed
Genome_build: T1 reference genome: ABIR00000000; T4 reference genome: PRJNA451013; Other reference genomes: PRJNA257433
Supplementary_files_format_and_content: rpkm Bed format
|
| |
|
| Submission date |
Nov 14, 2019 |
| Last update date |
Jun 01, 2021 |
| Contact name |
Yayan Feng |
| E-mail(s) |
[email protected]
|
| Phone |
13161164012
|
| Organization name |
Chinese Academy of Agricultural Sciences
|
| Lab |
Genome Analysis Laboratory of the Ministry of Agriculture
|
| Street address |
No. 7 pengfei road, dapeng new district, shenzhen
|
| City |
Shenzhen,Guangdong Province,China |
| State/province |
--- Select a state --- |
| ZIP/Postal code |
518000 |
| Country |
China |
| |
|
| Platform ID |
GPL27667 |
| Series (2) |
| GSE140382 |
12 transcriptomes of three life stages using RNA-Seq |
| GSE140384 |
Three life stages |
|
| Relations |
| BioSample |
SAMN13283391 |
| SRA |
SRX7141135 |
