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Status |
Public on Apr 24, 2024 |
Title |
CD4 T-cells, Theileria parva infected, day 69, 000035 |
Sample type |
SRA |
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|
Source name |
CD4 T-cells
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Organisms |
Theileria parva; Bos taurus |
Characteristics |
cell type: CD4 T-cells time: day 69 disease state: attenuated
|
Treatment protocol |
Cells were infected with saturating levels of fresh T. parva Muguga sporozoites.
|
Growth protocol |
Cells were maintained in RPMI-1640 medium supplemented with 10% FBS, 50mM beta-mercaptoethanol and 1X penicillin-streptomycin, in a humidified incubator at 37C and 5% CO2.
|
Extracted molecule |
total RNA |
Extraction protocol |
Total RNA was isolated using the miRNeasy kit (Qiagen). 500ng of total RNA was use for library preparation. The NEBNEXT Ultra II Directional RNA Library Prep kit was used with the Poly-A mRNA magnetic isolation module for library construction.
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|
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
NextSeq 2000 |
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|
Description |
S13_000035-D69
|
Data processing |
Quality control using FastQC (v 0.11.9 - default parameters) Trimming using TrimGalore (v 0.6.4) (--illumina --length 35 --paired) Pseudoalignment using kallisto (v 0.46.1 - default parameters - 10 bootstraps) Import of transcript-level abundances into R using tximport (v 1.24.0) Differential expression analysis using DESeq2 (v 1.36.0) Assembly: bosTau 9 (ARS-UCD1.2) and PiroplasmDB T. parva Muguga (GCA_000165365.1) Supplementary files format and content: Comma-separated values files with raw counts of Bos taurus genes for each sample Supplementary files format and content: Comma-separated values files with raw counts of Theileria parva genes for each sample
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Submission date |
Oct 12, 2023 |
Last update date |
Apr 24, 2024 |
Contact name |
Elisabeth Margaretha Diana Louise van der Heijden |
E-mail(s) |
elise.vanderheijden@ed.ac.uk
|
Organization name |
The Roslin Institute, The University of Edinburgh
|
Department |
Division of Immunology
|
Lab |
Connelley lab
|
Street address |
Easter Bush Campus
|
City |
Edinburgh |
State/province |
Midlothian |
ZIP/Postal code |
EH25 9RG |
Country |
United Kingdom |
|
|
Platform ID |
GPL33841 |
Series (1) |
GSE245180 |
Comparative transcriptional analysis identifies genes associated with the attenuation of Theileria parva infected cells after long-term in vitro culture |
|
Relations |
BioSample |
SAMN37795597 |
SRA |
SRX22075835 |