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sneddonucsf authored Jul 18, 2018
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Expand Up @@ -6,8 +6,10 @@ Scripts used for analysis of data in manuscript under revision at Nature Communi

seurat_v1.R - initialize seurat object from 10X Genomics cellranger outputs. Includes filtering, normalization, regression, variable gene identification, PCA analysis, clustering, tSNE visualization. Used for v1 datasets. <br /> <br />
merge_seurat.R - merge two or more seurat objects into one seurat object. Perform linear regression to remove batch effects from separate objects. Used for v1 datasets. <br /> <br />
subcluster_seurat_v1.R - Subcluster clusters of interest from Seurat object and reanalyze. Used for v1 dataset. <br /> <br />
seurat_v2.R - initialize seurat object from 10X Genomics cellranger outputs. Includes filtering, normalization, regression, variable gene identification, and PCA analysis. Used for v2 datasets. <br /><br />
clustering_markers_v2.R - clustering and tSNE visualization for v2 datasets. <br /><br />
subcluster_seurat_v2.R - Subcluster cluster of interest from Seurat object and reanalyze. Used for v2 dataset. <br /> <br />
seurat_object_analysis_v1_and_v2.R - downstream analysis and plotting functions for seurat object created by seurat_v1.R or seurat_v2.R. <br /><br />
merge_clusters.R - merge clusters that do not meet gene threshold. Used for both v1 and v2 datasets. <br /><br />
prepare_for_monocle_v1.R - subcluster cells of interest and perform linear regression, but not scaling in order to input normalized, regressed values into monocle with monocle_seurat_input_v1.R <br /><br />
Expand All @@ -17,53 +19,7 @@ monocle_object_analysis.R - downstream analysis for monocle object - BEAM and pl
CCA_merging_v2.R - script for merging v2 endocrine datasets with canonical correlation analysis and determining the number of CCs to include in downstream analysis. <br /><br />
CCA_alignment_v2.R - script for downstream alignment, clustering, tSNE visualization, and differential gene expression analysis.<br /><br />

# Object description

Seurat Objects - Generated by seurat_v1.R (V1 datasets) and seurat_v2.R scripts and clsutering_markers_v2.R (V2 datasets). Used for downstream analysis in seurat_object_analysis_v2_and_v2.R. <br /><br />

E14_allcells_seur_ob.Rdata - E14.5 V1 Dataset. Includes all cells. Seurat object. Grouped by "ordered_manuscript" in @data.info slot. Corresponds to Fig. 1c. <br /><br />

E14_mesenchyme_seur_ob.Rdata - E14.5 V1 Dataset. Only mesenchymal cells. Seurat object. Grouped by "ordered_manuscript" in @data.info slot. Corresponds to Fig. 2a. <br /><br />

merged_mesenchyme_seur_ob.Rdata - E12.5, E14.5, E17.5 merged V1 Dataset. Only mesenchymal cells. Seurat object. Grouped by "ordered_manuscript" in @data.info slot. Corresponds to Fig. 3a. <br /><br />

E14_epithelial_seur_ob.Rdata - E14.5 V1 Dataset. Only epithelial cells. Seurat object. Grouped by "ordered" in @data.info slot. Corresponds to Fig. 4a. <br /><br />

E14_endocrine_seur_ob.Rdata - E14.5 V1 Dataset. Only endocrine cells. Seurat object. Grouped by "ordered_res1_5" in @data.info slot. Corresponds to Fig. 4f. <br /><br />

merged_epithelial_seur_ob.Rdata - E12.5, E14.5, E17.5 merged V1 Dataset. Only epithelial cells. Seurat object. Grouped by "ordered" in @data.info slot. Corresponds to Supplementary Fig.5a <br /><br />

E12_v2_exocrine_seur_ob - E12.5 V2 Dataset. Only exocrine cells. Seurat object. Grouped by "merged" in @meta.data slot. Corresponds to Supplementary Fig. 5d <br /><br />

E14_v2_exocrine_seur_ob - E14.5 V2 Dataset. Only exocrine cells. Seurat object. Grouped by "merged" in @meta.data slot. Corresponds to Supplementary Fig. 5d <br /><br />

E17_v2_agg_exocrine_seur_ob - E17.5 aggregated V2 Dataset. Only exocrine cells. Seurat object. Grouped by "merged" in @meta.data slot. Corresponds to Supplementary Fig. 5d <br /><br />

E12_v2_endocrine_seur_ob - E12.5 V2 Dataset. Only endocrine cells. Seurat object. Grouped by "merged" in @meta.data slot. Corresponds to Supplementary Fig. 5e <br /><br />

E14_v2_endocrine_seur_ob - E14.5 V2 Dataset. Only endocrine cells. Seurat object. Grouped by "merged" in @meta.data slot. Corresponds to Supplementary Fig. 5e <br /><br />

E17_v2_agg_endocrine_seur_ob - E17.5 aggregated V2 Dataset. Only endocrine cells. Seurat object. Grouped by "merged" in @meta.data slot. Corresponds to Supplementary Fig. 5e <br /><br />

merged_v2_endocrine_seur_ob. - E12.5, E14.5, E17.5 (aggregated) V2 Dataset. Only endocrine cells. Seurat object. Grouped by "merged" in @meta.data slot. Corresponds to Fig. 5h. Generated by CCA_aligment_v2.R and CCA_merging_v2.R scripts. <br /><br />

E14_fev_lineage_endocrine_seur_ob. - E14.5 Fev-Cre;mTmG lineage traced V2 Dataset. Only endocrine cells. Seurat object. Grouped by "res.1.4" in @meta.data slot. Corresponds to Fig. 6h. "GFP" and "GFP_Bi" in @meta.data refer to GFP counts and binary "yes" or "no" for cells with >0 GFP counts.<br /><br />

Monocle objects - includes V1 seurat objects used for input (regression with no scaling) and resulting monocle object. For V2 Fev lineage traced dataset, same seurat object as listed above is used for input. <br /><br />

merge_meso_vsm_seur_ob - E12.5, E14.5, E17.5 V1 Dataset. Subclustered mesenchymal dataset for mesothelial and VSM populations. Prepared for monocle input by regression and no scaling analysis. Input for monocle_v1_seurat_input.R. <br /><br />

merge_meso_vsm_monocle_ob - Resulting monocle object generated from merge_meso_vsm_seur_ob. Used as input for monocle_object_analysis.R. Grouped by "final_clus" in phenoData. Corresponds to Fig. 3e. <br /><br />

E14_endocrine_mon_input_seur_ob - E14.5 endocrine V1 Dataset. Prepared for monocle, input into monocle_v1_seurat_input.R <br /><br />

E14_endocrine_monocle_ob - Resulting monocle object generated from E14_endocrine_mon_input_seur_ob. Grouped by "ordered_res1_5" in phenoData. Corresponds to Fig. 4g. <br /><br />

merge_fev_endocrine_seur_ob - E12.5, E14.5, E17.5 V1 Dataset. Subclustered epithelial dataset for Fev+/Pax4+, FevHi/Chgb+, Alpha, Beta, Epsilon, and Delta populations. Prepared for monocle, input into monocle_v1_seurat_input.R <br /><br />

merge_fev_endocrine_monocle_ob - Resulting monocle object generated from merge_fev_endocrine_seur_ob. Grouped by "merged_clus" in phenoData. Corresponds to Supplementary Fig. 8a. <br /><br />

E14_fev_lineage_monocle_ob - Resulting monocle objected generated from E14_fev_lineage_endocrine_seur_ob. Used monocle_lineage_trace.R script. Grouped by "res.1.4" in phenoData. Corresponds to Fig. 7a.



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