Introduction

Code and data to measure the contribution of RNA stability to the misregulation of genes in Rett iPSC-derived neurons. Look up preprint paper for details.

Data

The data folder contains auxiliary sequence data, quantified genes based on pA sites from the polyA_DB 3 database PMID: 29069441 and quantified microRNAs.

R notebooks

1. process_counts_data.Rmd

   Estimate fold-changes in transcription rate, steady state abundance and mRNA half-lifes from drosophila normalized gene level counts data. Gene counts were obtained from as a sum of counts from all pA sites of a gene.

2. measure_global_HL.Rmd

   Average mRNA half-life between cell types based on saturation curve method.

3. buffering_of_TR.Rmd

   Buffering of transcription rate changes with mRNA half-life

4. train_random_forest_on_TR.Rmd

   Train the random forest classifier for transcription rate changes based on k-mer content of coding and gene body sequence.

5. microRNA_analysis.Rmd

   Normalize endogenous microRNA abundances with spike-in RNA.

6. construct_primir_annotation.Rmd

   Prepare pA sites annotations of primary microRNAs based on transcripts annotation from PMID: 26290535

7. transite_analysis.Rmd

   Identify sequence features of buffered mRNAs relative to mRNAs with a same direction of transcription rate shift.