The **scRNAseq basic** analysis was conducted according to the workflow outlined below:
The **scRNAseq basic** analysis was conducted according to the workflow outlined below:
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@@ -49,7 +49,7 @@ Scaling (with following variables to regress out: percent.mt + nCount_RNA and CC
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@@ -49,7 +49,7 @@ Scaling (with following variables to regress out: percent.mt + nCount_RNA and CC
Custom annotation of cells was then performed according to Sakurai classifcation and markers inspection providing two different annotations levels: Classification variable (more refined) and Population variable - less granular as shown in Fig2C.
Custom annotation of cells was then performed according to Sakurai classifcation and markers inspection providing two different annotations levels: Classification variable (more refined) and Population variable - less granular as shown in Fig2C.
The complete list of markers produced by FindAllMarkers seurat function for all resolutions and annotation varibles (logfc.threshold = 0, min.pct = 0.2) is included in Data file S2.
The complete list of markers produced by FindAllMarkers seurat function for all resolutions and annotation varibles (logfc.threshold = 0, min.pct = 0.2) is included in Data file S2.
see: (FindAllMarkers_Population_dataset_Fig2C.R)[http://www.bioinfotiget.it/gitlab/custom/zonari_mpbhscexp_2025/zonari_mpbhscexp_2025_scrnaseq/-/blob/main/FindAllMarkers_Population_dataset_Fig2C.R] and result in .rds format: **Full_GSEA_markers_Population.rds**
see: [FindAllMarkers_Population_dataset_Fig2C.R](http://www.bioinfotiget.it/gitlab/custom/zonari_mpbhscexp_2025/zonari_mpbhscexp_2025_scrnaseq/-/blob/main/FindAllMarkers_Population_dataset_Fig2C.R) and result in .rds format: [Full_GSEA_markers_Population.rds](http://www.bioinfotiget.it/gitlab/custom/zonari_mpbhscexp_2025/zonari_mpbhscexp_2025_scrnaseq/-/blob/main/Full_GSEA_markers_Population.rds)
#### Evaluation of expansion culture on mPB CD34+ cells
#### Evaluation of expansion culture on mPB CD34+ cells
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@@ -68,9 +68,9 @@ Lists of common up/down regulated genes across culture were used as input for OR
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@@ -68,9 +68,9 @@ Lists of common up/down regulated genes across culture were used as input for OR
clusterprofiler R package (v4.7.1)
clusterprofiler R package (v4.7.1)
Code details and input for Supplementary Figure 2 can be found in:
Code details and input for Supplementary Figure 2 can be found in:
