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| Status |
Public on Apr 18, 2024 |
| Title |
Male biol rep2 |
| Sample type |
SRA |
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| Source name |
yoelii 17XNL
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| Organism |
Plasmodium yoelii |
| Characteristics |
cell line: yoelii 17XNL
cell type: Male gametocyte
genotype: WT
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from 2×107sex-sorted gametocytes was extracted using TRIzol.
RNA integrity was checked with the Agilent 2100 Bioanalyzer. mRNA was then enriched by Oligo(dT) beads. The enriched mRNA was fragmented into short fragments using fragmentation buffer and reverse transcripted into cDNA with random primers. Second-strand cDNA were synthesized by DNA polymerase Ⅰ, RNase H, dNTP and buffer. The cDNA fragments were purified with the QIAQuick PCR Purification Kit, end-repaired, A tailed, and ligated to Illumina sequencing adapters. The ligation products were size-selected by agarose gel electrophoresis, PCR amplified, and sequenced using Illumina NovaSeq 6000 by Genedenovo Biotechnology Co., Ltd (Guangzhou, China).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
The reads obtained from the sequencing machines including adapters or low-quality bases were filtered by fastp (version 0.18.0).
The reads of ribosome RNA (rRNA) were removed by the short reads alignment tool Bowtie2 (version 2.2.8).
The remaining paired-end clean reads were aligned to the plasmodium genome using HISAT2.
Read counts per transcript were obtained by the HTSeq-Counts package with default parameters
Assembly: The mapped reads were assembled with StringTie v1.3.1
Supplementary files format and content: tab-delimited text files include FPKM values for each sample
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| Submission date |
Jan 13, 2023 |
| Last update date |
Apr 18, 2024 |
| Contact name |
jiepeng guan |
| E-mail(s) |
guanjiepengn@gmail.com
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| Organization name |
Xiamen University
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| Street address |
Xiamen University
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| City |
Xiamen |
| ZIP/Postal code |
361105 |
| Country |
China |
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| Platform ID |
GPL29225 |
| Series (1) |
| GSE222860 |
Plasmodium yoelii gender-specific gametocyte transcriptome |
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| Relations |
| BioSample |
SAMN32730172 |
| SRA |
SRX20376899 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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