|
| Status |
Public on May 24, 2021 |
| Title |
PyWTasexual-1 |
| Sample type |
SRA |
| |
|
| Source name |
Asexual blood stage sans gametocytes
|
| Organism |
Plasmodium yoelii |
| Characteristics |
strain: 17XNL
genotype: wild type
Stage: schizont
|
| Treatment protocol |
Parasites were purified by Accudenz discontinuous density gradient, treated with 0.1% w/v saponin (final) to lyse erythrocyte membranes, and then washed in 1xPBS.
|
| Growth protocol |
Plasmodium yoelii (17XNL strain) parasites were used to infect swiss webster mice. Gametocyte samples were produced by treatment of mice with sulfadiazine. Schizont samples with gametocytes depleted were produced by counter-selecting against magnetic parasites (trophozoites, schizonts, gametocytes) and collecting ring stage parasites. These ring stage parasites were allowed to grow and develop to schizonts ex vivo.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Parasite pellets were immediately subjected to the QIAgen Rneasy Kit with an additional on-column DNasI digestion step. RNA quality was assessed by Bioanalyzer.
A barcorded library was made with the Illumina TruSeq stranded mRNA library prep kit according to manufacturer's protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
Not1g vs WT Asexual RNA-seq.xlsx
|
| Data processing |
Hisat2: Samples were mapped to the reference genome (P. yoelii 17XNL strain, plasmodb.org v50)
FeatureCounts: Raw read counts for the annotated genes were obtained from the alignments using featureCounts (Version2.0.0)
DESeq2: Reads counts were normalized and differentially expressed genes between WT and NOT1-G knockout samples were obtained separately in different life stages using DESeq2.
Genome_build: All data sets were aligned to the P. yoelii 17XNL strain obtained from PlasmoDB version 50.
|
| |
|
| Submission date |
Aug 30, 2019 |
| Last update date |
May 24, 2021 |
| Contact name |
Scott E. Lindner |
| E-mail(s) |
[email protected]
|
| Phone |
8148674062
|
| Organization name |
Penn State University
|
| Department |
Biochemistry and Molecular Biology
|
| Street address |
W224 Millennium Science Complex
|
| City |
University Park |
| State/province |
Pennsylvania |
| ZIP/Postal code |
16802 |
| Country |
USA |
| |
|
| Platform ID |
GPL21940 |
| Series (1) |
| GSE136674 |
Comparative RNA-seq of P. yoelii WT vs pynot1-g null parasites in schizont and gametocyte stages |
|
| Relations |
| BioSample |
SAMN12661905 |
| SRA |
SRX6777676 |
