This repository contains thefiles and scripts used for the analysis of embryogenesis time-course RNA-seq data, including tasks from expression quantification to summarisation and generatio of results figures. R packges used include ggplot2, dplyr, tidyverse, DESeq2 and RSubreads.
In 3_1_Transcriptomic data analysis.nb.html are the files and scripts to:
- Run gene expression quantification quantification at the gene, exon and intron level using FeaturesCounts (https://www.rdocumentation.org/packages/Rsubread/versions/1.22.2/topics/featureCounts)
- Run PCA analysis
- Run TPM normalisation across expression count matrix
- Test for epxression correlations between stages and library types
- Summarise stage-specific epxression
- To interpretate and generate figures showing main results
In 3_3 Maternal mRNAS - PolyA tail state analysis.nb.html are the files and scripts to:
- Identify set of matenrally provided mRNAs using expression thresholds
- Infere polyadenyaltion state by testing PolyA and Total expression fold change dynamics
- Cluster polyadenyation rate scores across developmental stage
- Test for epxression correlations between libraries for each identified cluster
In 3_4 Expression analysis during MZT.nb.html are the files and scripts to:
- Analyse trancriptome dynamics during embryogenesis by integrating PolyA and Total expression data
- Cluster gene expression across several developmenatl time-points
In 3_5 Zygotic genes - First expression.nb.html
- This notebook describes the identification of zygotic transcripts detected using the First Expression method. Briefly, zygotic genes were defined as those:
- Not maternally provided
- Significantly upregulated in each stage, usign as 0-9 hrs sample as reference timepoint
Please email [email protected] if there is any problem, thanks! (Manuel)
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