|
| Status |
Public on Mar 10, 2023 |
| Title |
Acanthaomeba castellanii, Mock |
| Sample type |
SRA |
| |
|
| Source name |
ATCC_30010
|
| Organism |
Acanthamoeba castellanii |
| Characteristics |
tissue: ATCC_30010
cell line: protist
cell type: T4
genotype: regular cuture
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The total RNA of A. castellanii was extracted with Direct-zolTM RNA MiniPrep (AYMO RESEAECH) according to the manufacturer’s protocol. The samples were treated with DNase I at 37°C for 30 minutes. DNase I was removed by phenol-chloroform extraction and total RNA was reprecipitated using sodium acetate and ethanol. The total RNA was eluted in nucleic acid-free water.
The protocol for strand-specific sample preparation was ScriptSeq v2 RNA-Seq Library Preparation Kit (Epicentre, USA).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
To determine gene expression profiles of amoeba, we also downloaded mRNA data (including 28,949 genes) from NCBI, followed by analysis with CLC Genomics Workbench (version 9.5.4).
The RNAseq data were first loaded into CLC, followed by trimming low quality sequence with the parameter specified: limit=0.05.
Mapping the reads after trimming to mRNA data set to determine gene expression profile with the default parameters.
|
| |
|
| Submission date |
Mar 10, 2023 |
| Last update date |
Mar 10, 2023 |
| Contact name |
Wei-Chen Lin |
| E-mail(s) |
wcnikelin@mail.ncku.edu.tw
|
| Organization name |
National Cheng Kung University
|
| Street address |
No.1, University Road
|
| City |
Tainan City |
| ZIP/Postal code |
701 |
| Country |
Taiwan |
| |
|
| Platform ID |
GPL33242 |
| Series (1) |
| GSE227112 |
Gene expression of Acanthamoeba castellanii under long-term co-culture condition |
|
| Relations |
| BioSample |
SAMN33715787 |
| SRA |
SRX19635537 |
