Project description:The goal of RNA-seq is to identify the differential expressed genes in the wild-type D.discoideum at different developmental stages (vegetative, streaming, mound and fruiting bodyies). Two biological replicates were assigned for each group and in total 8 groups were prepared for RNA-seq libraries with 500 ng mRNA as starting materials using NEXTflex Illumina qRNA-Seq Library Prep Kit (Bioo Scientific). We mapped about 20 - 30 million reads per sample to D. discoideum with bowtie2 workflow. The analysis pipeline started with pseudo-alignment of the reads using kallisto, followed by building an index and quantification process, which generated h5 files containing the raw binary files for preliminary differential analysis in sleuth. Differential analysis were conducted in EdgeR. The significant genes were deducted by computing NB exact genewise tests with corrected p < 0.05. Our results showed stage-specific gene expression profiles in different developmental stages.
Project description:To investigate the expression profile of three different developental stages of zebrafish embryos, we then performed gene expression profiling analysis using data obtained from RNA-seq of 3 different developmental of zebrafish embryos.
Project description:Cotton fiber were used for the expression analysis at different developmental stages Affymetrix Cotton Genome array were used for the global profiling of gene expression of cotton fiber at different developmental stages
Project description:This SuperSeries is composed of the following subset Series: GSE16733: Analysis of Gene Expression in Tissues of Two Turmeric Varieties at Different Developmental Stages GSE16734: Analysis of Gene Expression in Ginger Tissues at Different Developmental Stages Refer to individual Series
Project description:The goal of scRNA-seq is to identify the differential expressed genes in the wild-type D. discoideum at different developmental stages (vegetative, streaming, slug and fruiting bodies). Three biological replicates were assigned for each group and in total 12 groups were prepared for scRNA-seq libraries with 10000 cells as starting materials using Chromium Single Cell Gene Expression kit V3 (10x Genomics). Each sample was sequenced to an average of 393 million reads per sample with Illumina Hiseq 4000 and Novaseq 6000 platforms. The raw fastq files were processed by Cell Ranger (v 3.1.0, all with default setting except --normalize=none for aggr function) to generate the cell-barcode matrix. All downstreaming analysis was performed on R (3.6.3). Seurat package (3.1.5) was mainly used for basic analysis. Slingshot package was use for pseudotime analysis.
Project description:We investigated whether cell transplantation potential differs between the different developmental stages of the lungs. We found that epithelial cells derived from different developmental stages show different engraftment potential. To identify transcriptional signatures of epithelial cells that are associated with the phenomenon, we performed a time series transcriptome analysis of epithelial cells of the developing lungs.