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Integrate signatory data

[Music] hi guys welcome back to my channel i'm so happy to see you all here so today's video we'll talk about integrating single cell rna sequencing data sets in our using sarat package for this tutorial we will be using a hepatoglustoma dataset so hepatoblastoma is a pediatric cancer essentially these are tumors originating in the cells in the liver and the goal of the study is to identify distinct tumor cell populations and understanding key genetic mechanisms are through single cell rna sequencing and the design of the experiment is that samples are collected from three patients as you can see here in the table and the samples are collected from distinct sites so samples are collected from the actual hepatoplastoma tumor uh the background liver that is the tissue adjacent to the hepatoblastoma tumor and the patient derived xenografts so pdxs are actually when the tumors are extracted from the patients and inoculated and grown in mice as you can see here and these serve as a good model to study the growth and progression of the tumors single cell rna sequencing was then performed on these samples from each of these patients and the goal remains to identify distinct cell populations and understanding the heterogeneity and also understanding how they play a role in pathogenesis and intracellular signaling in hepatoblastoma however the goal of our analysis is to integrate data from these different patients and correct for the batch effects today we will talk about what are the different scenarios where we could use integration talk about different types of integration then i want to show you a list of batch correction methods available and finally demonstrate how to integrate the data talking about when to integrate integration can be used when you have multiple rna sequencing datasets from different conditions or different treatments or maybe different samples or different patients uh you can also use integration uh for cell label transfer so let's say if you have a well annotated uh data set you can use that as a reference to transfer the cell labels or annotations to the query data set uh integration can also be used for multimodal uh data sets uh so if you have a single cell rna-seq and single cell ataxic you can use integration to merge the different modalities uh and also you can use integration to integrate topological arrangement in cells with their gene expression for our tutorial the first case is more applying since we have uh similar cells uh similar measurements from different patients we can use integration to integrate the data from different patients and correct for the batch effects talking about the types of integration uh we have three types of integration so the first one is the horizontal integration where we have the same modality being measured across a different or independent group of cells so an example could be we could have rna sequencing performed on the same type of tissue but...