|
| Status |
Public on Jun 14, 2024 |
| Title |
IT4 SLI-var16 |
| Sample type |
SRA |
| |
|
| Source name |
P. f. infected human erythrocytes
|
| Organism |
Plasmodium falciparum |
| Characteristics |
tissue: P. f. infected human erythrocytes
cell line: IT4/FCR3
genotype: SLI integrant
|
| Growth protocol |
P. falciparum parasites (3D7 (Walliker et al., 1987) and IT4 (Jensen and Trager, 1978) were cultured using standard procedures (Trager and Jensen, 1976). The parasites were maintained in RPMI1640 supplemented with 0.5% Albumax and human 0+ erythrocytes, at a haematocrit of 5% at 37°C under an atmosphere consisting of 1% O2, 5% CO2, and 94% N2.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Synchronous ring-stage parasites with a parasitemia of 3 - 5%, dissolved in 5 pellet volumes of Trizol (Thermo Fischer). RNA isolation with Qiagen miRNeasy Mini Kit according to the manufacturer’s instructions. RNA integrity was assessed using the Agilent 2100® bioanalyzer system with the RNA 6000 Pico Kit. All samples had a RIN > 8.
Ribosomal RNA was removed using QIAseq FastSelect RNA Removal Kit. Libraries were prepared with the QIASeq Stranded mRNA Library Kit and sequenced on an Illumina NextSeq 550 system with NextSeq 500/550 Mid Output Kit v2.5 (150 cycles).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 550 |
| |
|
| Description |
var16_3
|
| Data processing |
Raw reads were mapped with hisat2 (version 2.2.1) to the respective reference genomes sourced from PlasmoDB (Amos et al., 2022). Mapped reads were sorted and indexed with samtools (version 1.17). Reads mapped to genomic features were counted using featureCounts (version 2.0.4). For var genes, only reads mapping to exon 1 were considered, for rifs, reads to the entire coding region were included. Python3 (version 3.11.4) and bioinfokit (version 2.1.2) were used to normalize the reads to transcripts per million (TPM).Differential gene expression analysis for panned against unpanned parasites was performed in R with the DESeq2 (version 1.42.0) package.
Assembly: IT4: Release 58; 3D7: Release 62
Supplementary files format and content: processed_data.xlsx; featureCounts, DESeq2
|
| |
|
| Submission date |
May 14, 2024 |
| Last update date |
Jun 14, 2024 |
| Contact name |
Johannes Allweier |
| E-mail(s) |
johannes.allweier@bnitm.de
|
| Organization name |
Bernhard Nocht Institute for Tropical Medicine
|
| Street address |
Bernhard-Nocht-Straße 74
|
| City |
Hamburg |
| ZIP/Postal code |
20359 |
| Country |
Germany |
| |
|
| Platform ID |
GPL26920 |
| Series (1) |
| GSE267413 |
A system for functional studies of the major virulence factor of malaria parasites |
|
| Relations |
| BioSample |
SAMN41392488 |
| SRA |
SRX24546075 |
