|
| Status |
Public on Jan 15, 2020 |
| Title |
Infected tachyzoite foreskin fibroblast (24 hours) replicate 1 |
| Sample type |
SRA |
| |
|
| Source name |
Foreskin
|
| Organisms |
Toxoplasma gondii; Homo sapiens |
| Characteristics |
infection: Infected
toxoplasma stage: Tachyzoite
toxoplasma strain: Prugniaud - Toxofilin-Cre (Koshy et al., 2010)
incubation time: 24 hours
incubation media: D1 - Dulbecco's Modified Eagle medium supplemented with 1% v/v fetal calf serum and 1% v/v Glutamax
|
| Treatment protocol |
host cells were washed with PBS and dislodged with trypsin before being FACS sorted for the presence of mCherry.
|
| Growth protocol |
Parasites were lysised and incoluated (or not) onto confluent HFF (host cells) at an MOI of 0.2 in either D1 ot iM media for 24 hours or 1 week.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using the RNeasy kit (Qiagen)
100ng of total RNA was prepared and indexed separately for IlluminaTM sequencing using the TruSeq RNA sample Prep Kit (Illumina) as per manufacturer’s instruction. Each library was quantified using the Agilent Tapestation and the Qubit™ DNA BR assay kit for Qubit 3.0® Fluorometer (Life technologies). The indexed libraries were pooled and diluted to 1.5pM for paired end sequencing (2x 81 cycles) on a NextSeq 500 instrument using the v2 150 cycle High Output kit (Illumina) as per manufacturer’s instructions (generating 80bp paired-ends)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
The base calling and quality scoring were determined using Real-Time Analysis on board software v2.4.6
The human and toxoplasma genomes were combined. Reads were aligned to this combined genome by Rsubread version 1.24.1
Reads counts were summarized using the Rsubread featureCounts function. Human genes were identified by Entrez Gene ID and NCBI annotation. Toxoplasma genes were identified using annotation available through ToxoDB (http://toxodb.org/toxo/)
Genome_build: hg38 (Homo sapien), ME49 (Toxoplasma gondii)
Supplementary_files_format_and_content: tab-delimited text files wre written from the R prompt; columns represent Entrez Gene ID (human)/ToxoDB ID (Toxoplasma), total gene length (total base count of all exons) and the number of reads mapping to that gene
|
| |
|
| Submission date |
Jan 15, 2019 |
| Last update date |
Jan 16, 2020 |
| Contact name |
Alexandra Garnham |
| E-mail(s) |
garnham.a@wehi.edu.au
|
| Organization name |
Walter and Eliza Hall Institute of Medical Research
|
| Street address |
1G Royal Parade
|
| City |
Parkville |
| State/province |
Victoria |
| ZIP/Postal code |
3052 |
| Country |
Australia |
| |
|
| Platform ID |
GPL26044 |
| Series (2) |
| GSE125121 |
RNA sequencing of host transcriptome of human foreskin fibroblast cells infected with either bradyzoites and tachyzoite of Toxoplasma gondii |
| GSE125122 |
Toxoplasma gondii bradyzoites manipulate host cell transcription |
|
| Relations |
| BioSample |
SAMN10751897 |
| SRA |
SRX5251551 |
