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| Status |
Public on Oct 17, 2019 |
| Title |
PfDis3-ADAR_T_rep2_TRIBE |
| Sample type |
SRA |
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| Source name |
malaria at Trophozoite
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| Organism |
Plasmodium falciparum |
| Characteristics |
developmental stage: Trophozoite
genotype: transgenic Pfdis3-ADAR
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| Extracted molecule |
total RNA |
| Extraction protocol |
Red blood cells infected by highly synchronous parasites were collected by centrifugation and resuspended in trizol that could be stored in -80℃ for a long time. After centrifugation, the supernatant was saved and then RNA was extracted according to reagent specification of Direct-zol™ RNA MiniPrep (R2052). The integrality of RNA was validated by 2% agarose gel.
Construction library was performed based on KAPA Stranded mRNA-Seq Kit (KK8421).
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| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
HiSeq X Ten |
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| Data processing |
Library strategy: TRIBE
Illumina Casava1.8 software used for basecalling.
pair end sequencing reads were trimmed with cutadapt (v11) by 10bp at each end, reads with average quality score >= 20 and length >=50bp were kept. Genomic DNA reads were aligned using bowtie2 (v2.2.5) (parameters: --sensitive) to the P.falciparum genome (plasmoDB.org, v3 release 32)[29]. Strand specific RNA sequencing reads were aligned using Tophat2 (v2.1.1) (parameters: -m 1 –g 2 -I 50000 --microexon-search --no-coverage-search --library-type fr-firststrand). PCR duplicates were removed for editing analysis.
Only events with minimum 10 and 5% editing were considered to be valid editing events. gDNA coverage>=30 and uniformity of nucleotide were also required to avoid single nucleotide polymorphisms (SNP). As biological replicates of the same treatment and developmental stage were highly correlated based on percentage editing, we combined them for the downstream analysis. RNA editing data is converted to bedgraph file format for display using R (v3.5.1).
Genome_build: PF3D7_32
Supplementary_files_format_and_content: bedgraph files indicating the editing sites of Pfdis3-ADAR
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| Submission date |
Jul 01, 2019 |
| Last update date |
Oct 17, 2019 |
| Contact name |
meng liu |
| E-mail(s) |
1710949@tongji.edu.cn
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| Organization name |
TongJi University
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| Street address |
1239,SiPing Road
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| City |
shanghai |
| ZIP/Postal code |
20082 |
| Country |
China |
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| Platform ID |
GPL26835 |
| Series (2) |
| GSE133653 |
TRIBE uncovers the role of Dis3 in shaping the dynamic transcriptome in malaria parasites [TRIBE] |
| GSE133654 |
TRIBE uncovers the role of Dis3 in shaping the dynamic transcriptome in malaria parasites |
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| Relations |
| BioSample |
SAMN12175132 |
| SRA |
SRX6386800 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3914207_TRIB_T_rep1_as.bedgraph.gz |
32.3 Kb |
(ftp)(http) |
BEDGRAPH |
| GSM3914207_TRIB_T_rep1_s.bedgraph.gz |
32.1 Kb |
(ftp)(http) |
BEDGRAPH |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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