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index.Rmd
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index.Rmd
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---
title: "Home"
site: workflowr::wflow_site
output:
workflowr::wflow_html:
toc: false
editor_options:
chunk_output_type: console
---
# Analysis of scRNA and bulk RNA sequencing data for "Characterizing gene expression responses to biomechanical strain in an in vitro model of osteoarthritis" project.
LCL-derived iPSCs from 3 Yoruba individuals were differentiated into mesenchymal stem cells and subsequently into chondrocytes. iPSC-derived chondrocytes were either placed under control conditions or treated with cyclic tensile strain for 24 hours (Total of 6 individual x treatment pairs). 3 technical replicates of the MSC-chondrocyte differentiation + strain/control treatment were conducted.Single cell RNAseq using the 10x platform was conducted for one replicate of the experiment (collection of one sample failed, meaning only 5 samples were single-cell sequenced). Bulk RNA sequencing was conducted for all 3 technical replicates.
If you are running the files in this repository to recreate the analyses, running them in the order they appear on this list is recommended.
## Single-cell data
* [Pre-processing of raw 10x files into count matrices and demultiplexing](preProcess_scRNA.html)
+ Figure S3
* [Integration and clustering of scRNA sequencing data](clustering_scRNA.html)
+ Figures 2B, 2C, 2D
* [Aggregation of external scRNA-seq data for topic model](external_scRNA.html)
* [Fitting and interpreting topic model with external data](topicModel_scRNA.html)
+ Figure 2A, S4, S5
## Bulk Data
* [Pre-processing of raw bulk RNA sequencing files](preProcess_bulkRNA.html)
* [Download Gene Annotations for GO analysis](download_gene_annotation.html)
* [Normalization and filtering of bulkRNAseq data](normFilter_bulkRNA.html)
+ Figure S10
* [Modeling and removing unwanted technical variation](removeUnwantedVariation_bulkRNA.html)
+ Figures 3A, 3B, S6, S8, S9
* [Differential expression using limma/voom](DEanalysis_bulkRNA.html)
+ Figure 4
* [Variance partitioning the bulk RNAseq data](variation_bulkRNA.html)
+ Figures 3C, S7
* [Selected examples of inter-individual heterogeneity](heterogeneity_bulkRNA.html)
+ Figure 5
## Power Analysis
* [Conducting power analysis for eQTL mapping](powerAnalysis.html)
+ Figure 6