Computational protocol: Maternal Germline-Specific Genes in the Asian Malaria Mosquito Anopheles stephensi: Characterization and Application for Disease Control

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Protocol publication

[…] RNA-Seq reads were mapped using TopHat () to all 11,789 predicted transcripts of the An. stephensi Indian strain (Assembly AsteI2, Geneset AsteI2.1; October 16, 2013; https://www.vectorbase.org/organisms/anopheles-stephensi). For this analysis, the nanos sequence ASTEI02887 was replaced with the coding region from AY738090.1 because it appeared the annotated transcript comprised two different genes. HTSeq () was used to generate mapped read counts for each transcript. Raw and RPKM-normalized () mapped RNA-Seq read counts can be found in Supporting Information, File S1. EdgeR () was used to identify differentially expressed genes (DEGs) by performing four pairwise comparisons between the 1- and 2-day-old previtellogenic ovary sample to four other samples (larvae, pupae, male, 24-hr PBM carcass). For the biological coefficient of variation, 0.4 was used as the single replicate samples were compared. From these outputs, two groups of DEGs were identified using false discovery rates (FDRs) of 0.001 and 0.01. Retaining the genes meeting the cutoff in all comparisons, 80 and 208 genes were identified, respectively (see File S2). Blast2GO () was used to annotate DEGs identified by EdgeR. All GO terms associated with each sequence can be found in File S3. […]

Pipeline specifications

Software tools TopHat, HTSeq, edgeR, Blast2GO
Databases VectorBase
Application RNA-seq analysis
Organisms Anopheles stephensi
Diseases Communicable Diseases, Malaria, Ovarian Neoplasms