Methods for time series analysis of rna-seq data with application to human th17 cell differentiation. Bioinformatics, 30(12):i113-i120, 2014.Aijo, T., Butty, V., Chen, Z., Salo, V., Tripathi, S., Burge, C. B., Lahesmaa, R., and Lahdesmaki, H. Methods for time series ...
Methods for time series analysis of RNA-seq data with application to human Th17 cell differentiation Methods for time series analysis of rna-seq data with application to human th17 cell differentiation. Bioinformatics. 2014; 30 (12):113–20. doi: ... Äijö Tarmo,B Vincent,C Zhi,... ...
RNA-seq analysis of an apical meristem time series reveals a critical point in Arabidopsis thaliana flower initiation. BMC Genomics, 2015, 16: 466.Klepikova AV, Logacheva MD, Dmitriev SE, et al. RNA-seq analysis of an apical meristem time series reveals a critical point in Arabidopsis ...
We used paired RNA-Seq and miRNA-Seq experiments to measure the mRNA and miRNA expression in bone marrow-derived macrophages over a time-series of 8 hours. Bioinformatics analysis identified 31 differentially expressed miRNAs between M1 and M2 polarized macrophages. The top 4 M1 miRNAs (miR-...
Differentially expressed (DE) genes in mouse M1 vs. M2 macrophages. (A) Principal Component Analysis (PCA) plot of 18 samples based on all detected genes in RNA-seq (B) Venn diagram of DE genes at 4 time points. (C) The time-series trends of 4 clusters of DE genes, where each line...
their response to cold or heat has not been studied. Here, we studied the transcriptome-level cold- and heat-shock response of spoilage lactic acid bacteria with time-series RNA-seq forLe. gelidum, Lc. piscium, andP. oligofermentansat 0 °C, 4 °C, 14 °C, 25 °C, and 28...
Inference of gene regulatory network structures from RNA-Seq data is challenging due to the nature of the data, as measurements take the form of counts of reads mapped to a given gene. Here we present a model for RNA-Seq time series data that applies a negative binomial distribution for the...
To investigate the intracellular kinetics of miRNA biogenesis (Figure 1A), we performed small RNA SLAMseq upon short pulse 4sU metabolic labeling in Drosophila S2 cells (for method validation see STAR Methods and Figure S1). To preempt confounding effects between the miRNA pathway and the RNAi pa...
In this study, we carried out time-series single-cell RNA sequencing (scRNA-seq) analyses of the shoots and roots of de-etiolatedArabidopsisseedlings and constructed a spatiotemporal cell atlas comprising 92,861 valid cells. The shoot cells displayed gradual but dramatic changes in transcriptional ...
STITCH assembles a graph manifold from time series single-cell RNA sequencing data. STITCH acknowledges that the gene expression signatures defining a complex biological process (e.g. embryonic development) can change dramatically over time. Rather than projecting data from several timepoints into a ...