|
| Status |
Public on Oct 14, 2024 |
| Title |
mixed blood stages, N67, rep 1 |
| Sample type |
SRA |
| |
|
| Source name |
Mixed blood stages
|
| Organism |
Plasmodium yoelii yoelii |
| Characteristics |
tissue: Mixed blood stages
genotype: N67
|
| Treatment protocol |
Briefly, iRBCs in 1 ml of 1.5 % sodium citrate/0.9% sodium chloride buffer were centrifuged at 500g for 5 min, resuspended in 1 ml PBS, and passed through two consecutive NWF filters (Zhixing Bio, Bengbu, China) to remove white blood cells
|
| Growth protocol |
Blood samples (200 ml) with approximately 30 ~ 40% parasitemia containing similar proportions of blood-stage parasites (ring, trophozoite, and schizont) were collected on day 4 after IP injection of mice with 1 × 106 iRBCs.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
iRBCs after NWF filter treatment were placed in RNA-later, and total RNAs were extracted using the Direct-zol™ RNA MiniPrep (Zymo Research) following the manufacturer's protocol
Five hundred nanograms of the total RNA was used to prepare the sequencing library using Illumina TruSeq Stranded mRNA library prep kits.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
LIB_NA_02064_01_01_S1
|
| Data processing |
Trim with Cutadapt v4.7
Map with STAR. v2.7.10b
Generate counts with RSEM v1.3.3
Differential expression with DESeq2
Assembly: P. yoelii yoelii N67C, PRJNA694977
Supplementary files format and content: raw counts matrix for all genes
|
| |
|
| Submission date |
Sep 27, 2024 |
| Last update date |
Oct 14, 2024 |
| Contact name |
Patrick Dolan |
| E-mail(s) |
[email protected]
|
| Phone |
301-761-7533
|
| Organization name |
National Institutes of Health
|
| Department |
National Institute of Allergy and Infectious Diseases
|
| Lab |
Laboratory of Viral Disease
|
| Street address |
33 NORTH DR RM 1E13C.4
|
| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20892 |
| Country |
USA |
| |
|
| Platform ID |
GPL34948 |
| Series (1) |
| GSE278246 |
Comparative genomics of Plasmodium yoelii nigeriensis N67 and N67C: Genome-wide polymorphisms, differential gene expression, and drug resistance |
|
| Relations |
| BioSample |
SAMN43965295 |
| SRA |
SRX26225769 |
