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Sample GSM7232571

Query DataSets for GSM7232571

Status

Public on Apr 18, 2024

Title

Py17XNL_MG_Rep3

Sample type

SRA

Source name

17XNL

Organism

Plasmodium yoelii

Characteristics

cell line: 17XNL
cell type: Male gametocyte
genotype: WT

Extracted molecule

polyA 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).

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina NovaSeq 6000

Data processing

The reads obtained from the sequencing machines including adapters or low-quality bases were filtered by trim-galore (version 0.6.10).
The reads of ribosome RNA (rRNA) were removed by hisat2 (version 2.2.1).
The remaining paired-end clean reads were aligned to the plasmodium genome using hisat2 (version 2.2.1)
Read counts per transcript were obtained by using featureCounts (version 2.0.3)
TPM values for each gene in each samples were calculated by using the R package t-arae/ngscmdr (version 0.1.0.181203)
Read counts TMM normalization and differential gene analysis were performed by using edgeR (version 3.16)
Assembly: GCA_900002385
Supplementary files format and content: csv files include TPM normalized for each Sample
Supplementary files format and content: csv files include log2FoldChange, p-values, FDR and TMM normalized counts generated from edgeR for each Sample

Submission date

Apr 26, 2023

Last update date

Apr 18, 2024

Contact name

jiepeng guan

E-mail(s)

guanjiepengn@gmail.com

Organization name

Xiamen University

Street address

Xiamen University