|
| Status |
Public on Mar 06, 2022 |
| Title |
3D7_AP2-HC-KO_S_RNA-seq, Rep3 |
| Sample type |
SRA |
| |
|
| Source name |
schizont (40-45 hpi)
|
| Organism |
Plasmodium falciparum |
| Characteristics |
tissue: whole body
developmental stage: schizont (40-45 hpi)
strain: Pf 3D7
genotype: AP2-HC-KO
host: Homo sapiens
|
| Treatment protocol |
Parasites were tightly synchronized to a 6-hour window by isolating schizonts over a 40% and 70% Percoll-sorbitol gradient followed by sorbitol treatment 6 hours post re-invasion.
|
| Growth protocol |
Parasites were cultured in fresh O-type human erythrocytes in complete RPMI 1640 medium (Gibco) with 0.5% Albumax I (Invitrogen) and a gas phase maintained under 5% CO2, 5% O2 and 90% N2 at 37°C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Highly synchronous parasites were collected in TRIzol at the ring (10-15 hpi), trophozoite (25-30 hpi), and schizont (40-45 hpi) stages from the next cycle, respectively. Total RNA purification was conducted with the Direct-zol RNA Kit (Zymo Research).
Libraries were prepared for strand-specific RNA sequencing by poly(A) selection with the KAPA mRNA Capture Beads (KAPA Biosystems) first and then RNA fragmentation to a size of 300-400 nucleotides. Subsequent library preparation steps followed the protocol of the KAPA Stranded mRNA-seq Kit Illumina platform (KAPA Biosystems, KK8421).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
| |
|
| Data processing |
To remove residual adapters and low-quality bases, sliding window trimming was performed on reads with Trimmomatic v0.39 using a window size of 4 and average quality of the window above 15. A minimum read length of 50 bp and average read quality above 20 were required after read clipping.
HISAT2 v2.2.1 was employed to align trimmed RNA-seq reads to the P. falciparum 3D7 reference genome (release 47) with the guide by the gene annotation, using default parameters except --max-intronlen 5000 --dta --rna-strandness RF.
StringTie v2.1.2 was used to count reads mapped to each gene.
Genome_build: Pf 3D7 v47
Supplementary_files_format_and_content: matrix table with raw gene counts for every gene and every sample
|
| |
|
| Submission date |
Sep 23, 2021 |
| Last update date |
Mar 06, 2022 |
| Contact name |
Mei Jiang |
| E-mail(s) |
gingerplum@hotmail.com
|
| Phone |
862165985138
|
| Organization name |
Tongji University
|
| Street address |
1239 Siping Road
|
| City |
Shanghai |
| State/province |
Shanghai |
| ZIP/Postal code |
200092 |
| Country |
China |
| |
|
| Platform ID |
GPL26835 |
| Series (2) |
| GSE184645 |
A coordinated regulatory network of ApiAP2 transcription factors involved in heterochromatic gene expression during Plasmodium falciparum blood-stage development [RNA-Seq] |
| GSE184659 |
A coordinated regulatory network of ApiAP2 transcription factors involved in heterochromatic gene expression during Plasmodium falciparum blood-stage development |
|
| Relations |
| BioSample |
SAMN21571807 |
| SRA |
SRX12306051 |
