From f7af63d0f5baae10c017cfc0c24b078fd96f2795 Mon Sep 17 00:00:00 2001 From: Adaikalavan Ramasamy Date: Fri, 6 Dec 2024 12:15:04 +0800 Subject: [PATCH 1/3] Update slides.html 1. Added a section on Why Cell Annotation is Important 2. Made textual edits to first seven slides. Went to lunch --- .../scrna-case-cell-annotation/slides.html | 25 +++++++++++++++---- 1 file changed, 20 insertions(+), 5 deletions(-) diff --git a/topics/single-cell/tutorials/scrna-case-cell-annotation/slides.html b/topics/single-cell/tutorials/scrna-case-cell-annotation/slides.html index 241bb2e5a83775..7b952994d40c46 100644 --- a/topics/single-cell/tutorials/scrna-case-cell-annotation/slides.html +++ b/topics/single-cell/tutorials/scrna-case-cell-annotation/slides.html @@ -36,11 +36,11 @@ ### What is Cell Annotation? -- Categorising cells into cell type categories based on transcriptomic data +- Classify cells in your data into different cell types based on gene expression data - Can be done manually or automatically -- Is possible due to single-cell sequencing technology +- Single-cell sequencing technology provides higher resolution than bulk RNA-seq ![Basic pipeline for automated cell annotation](../../images/scrna-cell-annotation/cell-annotation.png) @@ -52,9 +52,24 @@ --- -### Why is it Important? +### Why is Cell Annotation Important? -- Able to process and analyse single cell data much faster than manual analysis + +- To understand the composition of cell types in samples (cellular heterogeneity) + +- To compare changes in cell populations or states across different condition and phenotypes + +- To perform differential expression within each cell type to avoid signal dilution from mixed cell type population + +- To identify novel cell states and study some cell population further + +--- + +### Why Automate Cell Annotation? + +- Each single-cell experiments can generate data for thousands of cells + +- Manual annotation is time consuming and requires domain expertise - Can produce results more consistently allowing for reproducibility of results @@ -84,7 +99,7 @@ - Cell annotation uses sc-RNA seq data -- Gene expressions are stored in a gene expression matrix (X) +- Gene expressions are stored in a gene expression matrix (X)

Common data types: From 15287bd468e08c774af06c135d06c5909193b151 Mon Sep 17 00:00:00 2001 From: Adaikalavan Ramasamy Date: Fri, 6 Dec 2024 12:58:20 +0800 Subject: [PATCH 2/3] Update slides.html Added presenter notes to "Why cell type annotation is important" --- .../scrna-case-cell-annotation/slides.html | 24 +++++++++++++++---- 1 file changed, 20 insertions(+), 4 deletions(-) diff --git a/topics/single-cell/tutorials/scrna-case-cell-annotation/slides.html b/topics/single-cell/tutorials/scrna-case-cell-annotation/slides.html index 7b952994d40c46..c4ca28be1cd913 100644 --- a/topics/single-cell/tutorials/scrna-case-cell-annotation/slides.html +++ b/topics/single-cell/tutorials/scrna-case-cell-annotation/slides.html @@ -63,11 +63,22 @@ - To identify novel cell states and study some cell population further +??? + +The power of single-cell RNA-seq lies in its ability to capture the transcriptome at single-cell resolution. + +However, a significant challenge is accurately classifying cells into distinct types before beginning downstream analysis. + +Once cells are annotated, we can examine the composition of cell types within each sample and compare them across conditions. + +This precise classification enables differential expression analysis within specific cell types, a key objective of single-cell experiments. + + --- ### Why Automate Cell Annotation? -- Each single-cell experiments can generate data for thousands of cells +- Each single-cell experiment can generate data for thousands of cells - Manual annotation is time consuming and requires domain expertise @@ -121,14 +132,19 @@ --- -### Challenges +### Challenges in Automated Cell Type Annotation + +- Noise due to amplification techniques, varying sequencing depths, and sequencing errors -- Data is often noisy due to amplification techniques, varying sequencing depths, and errors in the reads +- Difference in QC steps for reference and query dataset may introduce a bias - Cell type definitions are inherently subjective and may be suboptimal +- Lack of a suitable reference panel for the query dataset can result in inaccurate classification, especially when dealing with unknown cell states + - Dealing with unknown cell types due to undiscovered classifications + ??? There are some challenges that need to be faced in order to perform automated cell annotation: @@ -143,7 +159,7 @@ ### Manual Cell Annotation -- Generate a cluster map and manually annotate each clusters +- Generate a cluster map and manually annotate each cluster - Requires the researchers to find known marker genes in the data From 51efa6bfeb0cf025e46deaa2eb8ff7f743a7c287 Mon Sep 17 00:00:00 2001 From: Adaikalavan Ramasamy Date: Fri, 6 Dec 2024 13:04:48 +0800 Subject: [PATCH 3/3] Update slides.html Edited until Slide 10 --- .../tutorials/scrna-case-cell-annotation/slides.html | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/topics/single-cell/tutorials/scrna-case-cell-annotation/slides.html b/topics/single-cell/tutorials/scrna-case-cell-annotation/slides.html index c4ca28be1cd913..eb81eb7045fb88 100644 --- a/topics/single-cell/tutorials/scrna-case-cell-annotation/slides.html +++ b/topics/single-cell/tutorials/scrna-case-cell-annotation/slides.html @@ -159,9 +159,11 @@ ### Manual Cell Annotation -- Generate a cluster map and manually annotate each cluster +- Requires known marker genes for cell types of interest -- Requires the researchers to find known marker genes in the data +- Generate the UMAP/tSNE (see below) to visualize the expression values + +- If you have clustered the cells, you can use dotplots or violin plots to measure the average expression of these genes ![Various cell cluster diagrams showing the expression values of various marker genes](../../images/scrna-cell-annotation/manual-annotation.png) @@ -185,7 +187,7 @@ .pull-left[ -- The process of identifying unique gene expressions that can be used for identifying cell types +- The process of identifying genes that are uniquely expressed in certain cell types - Genes are selected based on how differently they are expressed across different cell types