|
| Status |
Public on Aug 03, 2021 |
| Title |
pfap2-g5_dDBD_3D7_WGS-seq |
| Sample type |
SRA |
| |
|
| Source name |
pfap2-g5_dDBD_3D7_WGS-seq
|
| Organism |
Plasmodium falciparum |
| Characteristics |
development stage: Trophozoite (30-40hpi)
strain: Pf 3D7
genotype: pfap2-g5_dDBD
host: Homo sapiens
|
| Treatment protocol |
The medium was changed every other day until parasitaemia rose to 5%.
|
| Growth protocol |
Parasites were cultured in medium containing 0.5% Albumax II with O type fresh red blood cells, and a gas phase with 5% O2, 5 % CO2 at 37 °C.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted according to the DNeasy Blood and Tissue Kit (QIAGEN) manufacturer's requirements.
Genomic DNA samples were randomly broken into fragments of 350 bp length by Covaris ultrasonic disruptor. TruSeq Library Construction Kit was used for library construction. The entire library preparation was completed by end repair, addition of ployA tails, addition of adaptors, purification, and PCR amplification. The libraries were sequenced by illumina.
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
HiSeq X Ten |
| |
|
| Data processing |
Library strategy: WGS-seq
Low-quality and the adaptor sequences were trimmed from the reads using cutadapt (v1.16) with parameters: -a AGATCGGAAGAGC -A AGATCGGAAGAGC --trim-n -m 50 -q 20,20.
Then, the reads were mapped to the Plasmodium falciparum 3D7 genome (Pf 3D7 v32, obtained from PlasmoDB) using BWA (v0.7.17) with parameters: mem -k 32 -M.
The Samtools (v1.9) was used to filter low mapping quality reads and transfer the mapping results from sam format to position sorted bam format.
Next, the duplicated reads were removed by markdup from sambamba (v0.6.8) .
The Samtools (v1.9) was used to perform SNP/InDel calling with parameters: mpileup -q 1 -C 50 -m 2 -F 0.002 -d 1000.Then we filtered this sets using the following criteria: the mapping quality >20 and the depth of the variate position >4.
ANNOVAR was used for functional annotation of variants. Vcftools (v0.1.16) was used for set comparison between samples.
Genome_build: Pf 3D7 v32
Supplementary_files_format_and_content: The final SNP/InDel sets of each sample were uploaded as supp.
|
| |
|
| Submission date |
Jun 01, 2021 |
| Last update date |
Aug 03, 2021 |
| Contact name |
Shijun Shen |
| E-mail(s) |
xiaoshen19930901@163.com
|
| Phone |
+86-21-13795384821
|
| Organization name |
Tongji University
|
| Department |
Bioninformatics
|
| Lab |
Jiang Lab
|
| Street address |
1239 Siping Road, Shanghai, P.R. China
|
| City |
Shanghai |
| State/province |
Shanghai |
| ZIP/Postal code |
200092 |
| Country |
China |
| |
|
| Platform ID |
GPL26835 |
| Series (2) |
| GSE149774 |
A transcriptional repressor programs gametocytogenesis in human malaria parasites (PfAP2-G5) |
| GSE175931 |
A transcriptional repressor programs gametocytogenesis in human malaria parasites (PfAP2-G5) [WGS-Seq] |
|
| Relations |
| BioSample |
SAMN19489252 |
| SRA |
SRX11040270 |
