Update README.md

README.md

@@ -30,7 +30,7 @@ DOI:
 ## Data analysis workflow
 ### Dataset Fig2C
 
-![Fig2C](https://www.dropbox.com/scl/fi/lzb8u6oj4bvd0xf6977aw/Dataset2C.png?rlkey=t0g2g067pr7ukcdludv3rgh8j&dl=1 =300x200)
+![Fig2C](https://www.dropbox.com/scl/fi/lzb8u6oj4bvd0xf6977aw/Dataset2C.png?rlkey=t0g2g067pr7ukcdludv3rgh8j&dl=1)
 
 Figures 2C,D,E,F : [Figures_2CDEF.R](http://www.bioinfotiget.it/gitlab/custom/zonari_mpbhscexp_2025/zonari_mpbhscexp_2025_scrnaseq/-/blob/main/Figures_2CDEF.R). 
 Figure 2G: [Figures_2G.R](http://www.bioinfotiget.it/gitlab/custom/zonari_mpbhscexp_2025/zonari_mpbhscexp_2025_scrnaseq/-/blob/main/Figures_2G.R). 
@@ -72,5 +72,20 @@ Code details and input for Supplementary Figure 2 can be found in:
 - [Supplemental_fig2_part2.R](http://www.bioinfotiget.it/gitlab/custom/zonari_mpbhscexp_2025/zonari_mpbhscexp_2025_scrnaseq/-/blob/main/Supplemental_fig2_part2.R)
 - [Supplemental_fig2_input.rds](http://www.bioinfotiget.it/gitlab/custom/zonari_mpbhscexp_2025/zonari_mpbhscexp_2025_scrnaseq/-/blob/main/Supplemental_fig2_input.rds)
 
+### Dataset Fig2H
+
+#### Basic analysis
+The **scRNAseq basic** analysis was conducted according to the workflow outlined below:
+
+1. QC: min.cells = 20; min_feature: between 200 and 6000; max pct.mito = 20.
+Normalization (default seurat settings)
+2. ALRA (Imputation with default parameters in RunALRA function)
+2. Scaling (with following variables to regress out: percent.mt + nCount_RNA and CC.Difference calculated as show in [vignette](https://satijalab.org/seurat/articles/cell_cycle_vignette.html#alternate-workflow-1))
+3. Dimensionality reduction: PCA (top 25PCs using 15% most variable genes of whole gene list)
+4. Harmony batch removal (sample/ orig.ident)
+5. Clustering (Louvain improved: algorithm number 2 in FindCluster Seurat function)
+
+
+