|
| Status |
Public on Jan 12, 2024 |
| Title |
P. berghei ANKA trophozoite stage cells, wild type, replicate 3 |
| Sample type |
SRA |
| |
|
| Source name |
Trophozoites
|
| Organism |
Plasmodium berghei |
| Characteristics |
cell type: Trophozoites
genotype: Wild type
|
| Treatment protocol |
The CAP knockout mutants were generated in PbA-NIH and PbA-SZ by transfecting a linearized DNA construct generated based on plasmid pL0034 (MRA-849, www.mr4.org) under the positive selection with pyrimethamine.
|
| Growth protocol |
Red blood cells infected by P. berghei ANKA parasites were injected into mice by intraperitoneal (i.p) injection. Trophozoite parasites were acquired by collecting blood at a parasitemia stage of 1-3%, followed by filtration, lysis with Red Blood Cell Lysis Buffer, and washing with PBS to isolate the parasites.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted and purified by RiboPureTM kit, and ribosomal RNA was removed using Illumina Ribo-Zero Plus rRNA Depletion Kit, and the rRNA-free residue was precipitated by ethanol
Sequencing libraries were generated using the rRNA-depleted RNA by NEB Next Ultra Directional RNA Library Prep Kit for Illumina (NEB, USA) following the manufacturer’s recommendations
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trimmomatic (v0.32) (default parameters)
Trimmed sequence reads were mapped to P. berghei genome (PlasmoDBv56) using STAR (v2.7.1a) with default parameters
Read count extraction were performed using GenomicAlignments (v1.24.0)
Read count extraction were normalization using DESeq2 (v1.24.0)
Assembly: P. berghei genome (PlasmoDBv56)
Supplementary files format and content: Tab-delimited txt files includes raw counts for each Sample
Supplementary files format and content: Tab-delimited txt files include RPKM values for each Sample
|
| |
|
| Submission date |
Jan 08, 2024 |
| Last update date |
Jan 12, 2024 |
| Contact name |
chen li |
| E-mail(s) |
chenli5679@126.com
|
| Organization name |
Sichuan Univercity
|
| Street address |
Renmin South Road
|
| City |
Chengdu |
| ZIP/Postal code |
610041 |
| Country |
China |
| |
|
| Platform ID |
GPL20293 |
| Series (1) |
| GSE252704 |
Malaria parasite manipulates erythrocyte membranes for intracellular adaptation : RNA-seq |
|
| Relations |
| BioSample |
SAMN39291031 |
| SRA |
SRX23128245 |
