|
| Status |
Public on Feb 14, 2024 |
| Title |
Febrile [2F] |
| Sample type |
SRA |
| |
|
| Source name |
host peripheral blood mononuclear cells (PBMCs)
|
| Organism |
Plasmodium falciparum 3D7 |
| Characteristics |
infection status: Febrile
tissue: host peripheral blood mononuclear cells (PBMCs)
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
using the ISOLATE II RNA Mini Kit (Bioline)
libraries for RNA-seq were prepared using the NEBNextTM Ultra II FS DNA library preparation kit (New England Biolabs) following manufacturers protocol
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
kwtrp_sims_14
|
| Data processing |
sequence reads were accessed for quality
Sequence reads were mapped to the reference Plasmodium falciparum (3D7 strain) from PlasmoDB, release 55, using Kallisto (default settings)
Genes with less that 2 counts per million in 10 or less samples were dropped
TMM Normalization was done
Assembly: 3D7 strain, PlasmoDB, release 55
Supplementary files format and content: tab-delimited file includes raw counts for each sample
Supplementary files format and content: tab-delimited file includes normalized counts for each sample
|
| |
|
| Submission date |
Aug 11, 2023 |
| Last update date |
Feb 14, 2024 |
| Contact name |
Kelvin Muteru Kimenyi |
| E-mail(s) |
kmuteru@kemri-wellcome.org, kmut2030@gmail.com
|
| Organization name |
University of Nairobi
|
| Department |
Biochemistry
|
| Lab |
Center for Biotechnology and Bioinformatics (CEBIB)
|
| Street address |
30197
|
| City |
Nairobi |
| ZIP/Postal code |
00100 |
| Country |
Kenya |
| |
|
| Platform ID |
GPL28887 |
| Series (1) |
| GSE240643 |
Distinct transcriptomic signatures define febrile malaria depending on initial infective states, asymptomatic or uninfected |
|
| Relations |
| BioSample |
SAMN36943630 |
| SRA |
SRX21336431 |
