|
| Status |
Public on Feb 21, 2023 |
| Title |
12658 |
| Sample type |
SRA |
| |
|
| Source name |
Mus musculus infected with Plasmodium_berghei_NK66
|
| Organisms |
Plasmodium berghei; Mus musculus |
| Characteristics |
treatment: NK65_C57-6
|
| Treatment protocol |
Both Pb ANKA and Pb NK65 parasites stocks were originally grown in C57BL/6 mice. To avoid non-parasite specific immune response against infected C57BL/6 RBCs in Balb/c animals, initial Pb ANKA stock was divided into two and injected into both C57BL/6 and Balb/c donor animals. These parasites were passaged three times in respective mouse strains in order to fully adapt the parasite into the host.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Mouse cheek blood samples were mixed with Trizol LS (Thermofisher) in 1:3 ratio and RNA was isolated according to manufacturer’s guidelines
TruSeq Total RNA-Seq, Globin-zero
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Illumina Casava1.7 software used for basecalling.
Raw fastq reads were trimmed of Illumina adapter sequences using cutadapt version 1.12
then trimmed and filtered for quality using the FASTX-Toolkit (Hannon Lab)
Remaining reads were aligned to Plasmodium using hisat2(https://www.nature.com/articles/s41587-019-0201-4)
Reads mapping to genes were counted using htseq-count (Anders et al., 2015)
Differential expression analysis was performed using the Bioconductor package DESeq2 (Love et al., 2014)
Assembly: GCF_900002375.1_PBANKA01 and GCA_900088445.1_PbNK65E
Supplementary files format and content: tab-delimited text files include deseq2 values for each Sample
|
| |
|
| Submission date |
Oct 12, 2022 |
| Last update date |
Feb 21, 2023 |
| Contact name |
Dan Sturdevant |
| E-mail(s) |
dsturdevant@niaid.nih.gov
|
| Phone |
4063639248
|
| Organization name |
NIH
|
| Department |
NIAID
|
| Lab |
RTS
|
| Street address |
903 S 4th street
|
| City |
Hamilton |
| State/province |
MT |
| ZIP/Postal code |
59840 |
| Country |
USA |
| |
|
| Platform ID |
GPL32741 |
| Series (1) |
| GSE215359 |
Cerebral malaria is regulated by host mediated changes in Plasmodium gene expression |
|
| Relations |
| BioSample |
SAMN31260996 |
| SRA |
SRX17869257 |
