|
| Status |
Public on May 26, 2021 |
| Title |
AA1701_FUP |
| Sample type |
SRA |
| |
|
| Source name |
FUP HbAA rep2 3 hours post-invasion
|
| Organism |
Plasmodium falciparum |
| Characteristics |
tissue: Plasmodium falciparum: asexual blood stage
strain: FUP
hemoglobin genotype: HbAA
parasite stage: Ring
hours post-invasion: 3
patient age: N/A
patient sex: N/A
abo: N/A
parasite density (parasites/ul): N/A
date: 1/31/2019
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from in vitro samples using Trizol reagent, and extracted from in vivo samples using Trizol LS. Kapa Stranded mRNA-seq library prep kit was used with at least 100 ng of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
In vitro time series - FUP
|
| Data processing |
Real Time Analysis (RTA3) was used for base calling on the NovaSeq6000
Sequenced reads were trimmed for adaptor sequence and low quality bases, then mapped to ASM276v2 transcriptome using Salmon with parameters -p 8 -g $GTF-file --validateMappings
Transcripts per kilobase of exon Per Megabase of library size (TPM) were extracted from each quantification file output by Salmon using tximport.
Genome_build: ASM276v2
Supplementary_files_format_and_content: comma-delimited text files include TPM values for each sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
|
| |
|
| Submission date |
Dec 14, 2020 |
| Last update date |
May 26, 2021 |
| Contact name |
Steve Taylor |
| E-mail(s) |
steve.taylor@duke.edu
|
| Organization name |
Duke University School of Medicine
|
| Department |
Division of Infectious Diseases
|
| Lab |
Taylor
|
| Street address |
303 Research Dr
|
| City |
Durham |
| State/province |
NC |
| ZIP/Postal code |
27710 |
| Country |
USA |
| |
|
| Platform ID |
GPL26836 |
| Series (1) |
| GSE163144 |
Impact of sickle cell trait hemoglobin on the intraerythrocytic transcriptional program of Plasmodium falciparum |
|
| Relations |
| BioSample |
SAMN17076119 |
| SRA |
SRX9682373 |
