|
| Status |
Public on Jun 24, 2020 |
| Title |
PfArp4_R_GlcN+_rep1_RNAseq |
| Sample type |
SRA |
| |
|
| Source name |
PfArp4_R_GlcN+_rep1_RNAseq
|
| Organism |
Plasmodium falciparum |
| Characteristics |
developmental stage: Ring
genotype: PfArp4_GlcN+
host: Homo sapiens
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
The experiment began to collect the highly synchronized Plasmodium, centrifuge and remove the supernatant, then the cells was lysed by adding 1:5 triazole. Next to depolymerize the proteins and nucleic acids in the cells to release them, and extract RNA according to reagent specification of Direct-zol RNA MiniPrep (R2052). The resullts of RNA extraction were verified on a 2% agarose gel.
The mRNA was enriched with magnetic beads with Oligo (dT). It has been optimized to isolate mature mRNA from total RNA by capturing twice using the KAPA mRNA Capture Beads. This experiment was performed using the KAPA Stranded mRNA-seq Kit. Here, the required fragment size for the experiment is 300-400 bp. It carried out the fragmentation and priming program as follows: 85°C 6min. In particular, some changes to the library amplification procedure have been made as follows: initial 98°C 45sec 1cycle; denaturation 98°C 15sec 14cycles; annealing 65°C 30sec 14cycles; extension 65°C 30sec 14cycles; final extension 65°C 5min 1cycle; hold 10°C 1cycle. Resuspend the dried beads in 22µl of RNase-free water to obtain the final library building results. The library were sequenced on an Illumina HiSeq Xten systerm with PE150 strategy.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
| |
|
| Data processing |
Low-quality and 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 Hisat2 strand-specific mode (v2.1.0) with parameters: --rna-strandness RF --dta --no-discordant --no-mixed --no-unal.
Mapped reads were subsequently assembled into transcripts guided by the PlasmoDB gff annotation files (Pf 3D7 v32) using featureCounts (v1.6.1) with parameters: -M -p -B -C for all; -s 2 for sense transcripts; -s 1 for antisense transcripts.
Genome_build: Pf 3D7 v32
Supplementary_files_format_and_content: The raw counts were calculated by featureCounts as described above.
|
| |
|
| Submission date |
Jan 17, 2020 |
| Last update date |
Jun 24, 2020 |
| Contact name |
Xinyu Cui |
| E-mail(s) |
1810992@tongji.edu.cn
|
| Phone |
19921890601
|
| Organization name |
Tongji University
|
| Street address |
Siping road
|
| City |
Shanghai |
| ZIP/Postal code |
200082 |
| Country |
China |
| |
|
| Platform ID |
GPL26835 |
| Series (2) |
| GSE143901 |
Actin-related protein Arp4 regulates euchromatic gene expression and development by H2A.Z deposition in blood-stage Plasmodium falciparum [RNA-seq] |
| GSE143902 |
Actin-related protein Arp4 regulates euchromatic gene expression and development by H2A.Z deposition in blood-stage Plasmodium falciparum |
|
| Relations |
| BioSample |
SAMN13880142 |
| SRA |
SRX7579924 |
