|
| Status |
Public on Sep 12, 2020 |
| Title |
The control of porcine alveoalr macrophages, repeat 2 [NC2] |
| Sample type |
SRA |
| |
|
| Source name |
porcine alveoalr macrophage
|
| Organism |
Sus scrofa |
| Characteristics |
cell line/strain: 3D4/21
cell type: porcine alveoalr macrophage
infrection condition: at 70-80 % confluency in T25 tissue culture flask, about 36 h
|
| Treatment protocol |
Tachyzoites freshly egressed from HFFs were harvested and filtered through 3.0 um membrane filters (Whatman). Pig alveolar macrophage was infected with 3 type of different strain’ tachyzoites (TgRH, TgME49 and TgHB1) at MOI equal to 5 (the ratio of tachyzoite and macrophage). The parasites and macrophage were harvested together by 0.05% trypsin digestion at 6h, 12h and 24h time point respectively. Each experimental group had 3 biological replicates.
|
| Growth protocol |
The cells (pig alveolar macrophages and HFF cells) and 3 different T.gondii strains (TgRH, TgMe49 and TgHB1) were cultured in DMEM with 10% or 2% FBS, 2 mM L-glutamine, 100 U/ml penicillin and 10μg/ml streptomycin, respectively. These all were maintained at 37℃ in 5% CO₂ incubator.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted individually from mixture samples using Transzol UP Reagent (TransGen Biotech) according to the manufacturer’s protocol.
The RNA library was generated using NEBNext® Ultra™ RNA Library Prep Kit following manufacturer’s recommendations.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
| |
|
| Data processing |
Illumina Casava 1.8 software was used for basecalling
Clean reads were obtained by removing low quality reads and reads containing adapter. The clean reads were aligned to toxoplasma gondii TgME49 genome or Sus scrofa genome through HISAT 2.0.4.
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 read counts values for each sample
|
| |
|
| Submission date |
Jun 26, 2020 |
| Last update date |
Sep 12, 2020 |
| Contact name |
Yanqin Zhou |
| E-mail(s) |
yanqinzhou@mail.hzau.edu.cn
|
| Organization name |
Huazhong agricultural university
|
| Street address |
No.1, Shizishan Street, Hongshan District
|
| City |
Wuhan |
| State/province |
Hubei province |
| ZIP/Postal code |
430070 |
| Country |
China |
| |
|
| Platform ID |
GPL22918 |
| Series (1) |
| GSE153330 |
Dual RNA-seq analysis of pig alveolar macrophage infected with china-isolated TgHB1 compared to TgRH and TgMe49 toxoplasma gondii standard strain |
|
| Relations |
| BioSample |
SAMN15377086 |
| SRA |
SRX8622134 |
