 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Sep 23, 2021 |
| Title |
Tachyzoite - 3 |
| Sample type |
SRA |
| |
|
| Source name |
Purified T. gondii 76K tachyzoites grown in HFF cells
|
| Organism |
Toxoplasma gondii |
| Characteristics |
tissue: Tachyzoite
|
| Growth protocol |
Intracellular parasite were grown for 1, 2, 4, 7 and 14 days
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extrated using TRIzol reagent according to manufacturer’s protocol.
Library preparation was performed using the TruSeq Stranded mRNA Sample Preparation kit (Illumina) according to the manufacturer’s instructions. Libraries were validated using a Fragment Analyzer and quantified by qPCR (ROCHE LightCycler 480).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Clusters were generated on a flow cell within a cBot using the Cluster Generation Kit (Illumina), and libraries were sequenced as 50-bp reads on a HiSeq 2000 using a Sequence By Synthesis (SBS) technique (Illumina).
Image analysis and base calling were performed using the HiSeq Control Software and Real-Time Analysis component. Demultiplexing was performed using Illumina’s conversion software (bcl2fastq 2.17). The quality of the data was assessed using FastQC from the Babraham Institute and the Illumina software Sequence Analysis Viewer (SAV). Potential contaminants were investigated with the FastQ Screen software from the Babraham Institute.
Datasets were aligned with HiSAT2 v2.1.0 against the T. gondii ME49 genome from (ToxoDB-39) and to the rat genome (Rattus norvegicus Rn6 (UCSC)). Final read alignments having more than three mismatches were discarded. Gene counting was performed using HTSeq-count 0.6.1p1 (union mode). Because the data come from a strand-specific assay, the read must be mapped to the opposite strand of the gene. Before statistical analysis, genes with less than 15 reads (combining all the analyzed samples) were filtered out. Differentially expressed genes were identified using the Bioconductor package edgeR 3.6.7. The data were normalized using the Relative Log Expression (RLE) normalization factors. Genes with adjusted p-values less than 5% (according to the FDR method from Benjamini-Hochberg) were declared differentially expressed.
|
| |
|
| Submission date |
Mar 08, 2021 |
| Last update date |
Sep 23, 2021 |
| Contact name |
Mathieu Gissot |
| Organization name |
CNRS
|
| Department |
CIIL- UMR 8204 - U1019
|
| Lab |
Biology of Apicomplexan Parasites
|
| Street address |
1, rue du Pr. calmette
|
| City |
Lille |
| ZIP/Postal code |
59000 |
| Country |
France |
| |
|
| Platform ID |
GPL23377 |
| Series (1) |
| GSE168465 |
Primary brain cell infection by Toxoplasma gondii reveals the dynamics of spontaneous bradyzoite differentiation and the extend of modification of neuron biology after infection |
|
| Relations |
| BioSample |
SAMN18206592 |
| SRA |
SRX10269530 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
|
|
|
|
 |
