|
| Status |
Public on Mar 11, 2020 |
| Title |
Mp2 |
| Sample type |
SRA |
| |
|
| Source name |
porcine alveolar macrophages
|
| Organism |
Sus scrofa |
| Characteristics |
cell type: porcine alveolar macrophages
cell line: 3D4/21
parasite strain: n/a
culture time: at 70-80 percent confluency in T25 tissue culture flask, about 36 h
cell type: porcine alveolar macrophages
|
| Treatment protocol |
the purified Me49 tachyzoites from HFFs were counted and used to infect porcine alveolar macrophages (MOI=5) for 1 h, the extracellualr parasites were washed away with PBS. The infected porcine alveolar macrophages were cultured for further 15 h. the porcine alveolar macrophages and Me49 controls were maintained under same conditions.
|
| Growth protocol |
the cells (porcine alveolar macrophages and HFF cells) and Me49 tachyzoites were cultured in DMEM with 10% or 2% FBS, 2 mM L-glutamine, 100 U/ml penicillin and 100 μg/ml streptomycin, respectively. Both maintained in incubator with 5% CO₂ and kept 37℃.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
At indicated time, the samples were collected and total RNA was harvested using Trizol reagent. NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) was used with 3 µg total RNA per sample for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
| |
|
| Description |
Mp _abundance measurements.txt
|
| Data processing |
Illumina Casava 1.8 software was used for basecalling
sequenced reads were trimmed for adaptor sequence, reads containing ploy-N and low quality reads. Then clean reads were mapped to Sus scrofa or Toxoplasma reference genome by using TopHat v2.0.12.
Genome_build: Sus scrofa reference genone for alignment: ftp://ftp.ensembl.org/pub/current_fasta/sus_scrofa/dna/ ; Me49 reference genome for alignment: ftp://ftp.ensemblgenomes.org/pub/release-23/protists//fasta/toxoplasma gondii/dna/
Supplementary_files_format_and_content: tab-delimited text files include reads counts values for each sample
|
| |
|
| Submission date |
Mar 10, 2020 |
| Last update date |
Mar 11, 2020 |
| Contact name |
Bang Shen |
| E-mail(s) |
shenbang@mail.hzau.edu.cn
|
| Phone |
+86-27-87281810
|
| Organization name |
Huazhong Agricultural University
|
| Street address |
No. 1 SHizishan St
|
| City |
Wuhan |
| ZIP/Postal code |
430070 |
| Country |
China |
| |
|
| Platform ID |
GPL22918 |
| Series (1) |
| GSE146715 |
Dual RNA-seq analyses of porcine alveolar macrophage and Toxoplasma during infection process |
|
| Relations |
| BioSample |
SAMN14343663 |
| SRA |
SRX7886953 |
