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Sample GSM7838094 Query DataSets for GSM7838094
Status Public on Apr 24, 2024
Title CD4 T-cells, Theileria parva infected, day 69, 000035
Sample type SRA
 
Source name CD4 T-cells
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.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model NextSeq 2000
 
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
 
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

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA

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