Santhosh Sivajothi
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View article: KAPP-Sen TMC: Xenium - Cell DIVE - H&E v1
KAPP-Sen TMC: Xenium - Cell DIVE - H&E v1 Open
This protocol describes tissue section preparation, in situ spatial transcriptomic analysis, antibody-based imaging and H&E staining of tissue sections using an integrated workflow. Standardized procedures were followed for tissue processi…
View article: STAMP: Single-cell transcriptomics analysis and multimodal profiling through imaging
STAMP: Single-cell transcriptomics analysis and multimodal profiling through imaging Open
Single-cell RNA sequencing has revolutionized our understanding of cellular diversity but remains constrained by scalability, high costs, and the destruction of cells during analysis. To overcome these challenges, we developed STAMP (singl…
View article: KAPP-Sen TMC: 10x Xenium V1 with Segmentation Kit v1
KAPP-Sen TMC: 10x Xenium V1 with Segmentation Kit v1 Open
This protocol describes the preparation, staining, and in situ spatial transcriptomic analysis of tissue sections using an integrated 10x Genomics workflow. Standardized procedures were followed for tissue processing, slide preparation, an…
View article: Prediction of Outcome from Spatial Protein Profiling of Triple-Negative Breast Cancers
Prediction of Outcome from Spatial Protein Profiling of Triple-Negative Breast Cancers Open
In tumors, reciprocal spatial interactions between immune cells, their mediators, the extracellular matrix, and mutated neoplastic cells impact all aspects of treatment resistance. The operational mechanisms of these interactions are found…
View article: KAPP-Sen TMC:Routine H&E Processing and Staining using Leica ST5010 AutoStainer v1
KAPP-Sen TMC:Routine H&E Processing and Staining using Leica ST5010 AutoStainer v1 Open
This protocol details steps for tissue handling and sectioning, routine H&E staining using the Leica ST5010 AutoStainer XL, and imaging using the NanoZoomer-SQ digital slide scanner. This procedure applies to the members of the Single Cell…
View article: KAPP-Sen TMC: Tissue Sectioning Guidelines (FFPE) - CODEX/PhenoCycler v1
KAPP-Sen TMC: Tissue Sectioning Guidelines (FFPE) - CODEX/PhenoCycler v1 Open
The purpose of this SOP is to provide general guidelines for preparing FFPE tissue sections suitable for PhenoCycler/CODEX
View article: KAPP-Sen TMC:Xenium Pancreas FFPE Tissue Preparation v1
KAPP-Sen TMC:Xenium Pancreas FFPE Tissue Preparation v1 Open
Xenium protocol for sectioning FFPE tissue blocks.
View article: Hematoxylin and Eosin (H&E) Staining of Tissues following Multiplexed Imaging on Phenocycler-Fusion v1
Hematoxylin and Eosin (H&E) Staining of Tissues following Multiplexed Imaging on Phenocycler-Fusion v1 Open
Phenocycler-Fusion assay enables multiplexed antibody based imaging of FFPE or fresh frozen tissues. Hematoxylin and Eosin (H&E) staining is a gold standard method for observing tissue morphology. Obtaining multiplexed protein expression i…
View article: FFPE Tissue Processing for Multimodal Imaging Assays (Phenocycler-Fusion + H&E) following Xenium In Situ Gene Expression v1
FFPE Tissue Processing for Multimodal Imaging Assays (Phenocycler-Fusion + H&E) following Xenium In Situ Gene Expression v1 Open
Xenium In Situ Gene Expression assay from 10X Genomics enables multiplexed imaging of RNA transcripts in situ. There are several antibody based multiplexed imaging technologies that enable multiplexed protein detection. Hematoxylin and Eos…
View article: Tissue Sectioning Guidelines (FFPE) - CODEX/PhenoCycler v2
Tissue Sectioning Guidelines (FFPE) - CODEX/PhenoCycler v2 Open
The purpose of this SOP is to provide general guidelines for preparing FFPE tissue sections suitable for PhenoCycler/CODEX
View article: Tissue Sectioning Guidelines (Fresh Frozen)- CODEX/Phenocycler-Fusion v1
Tissue Sectioning Guidelines (Fresh Frozen)- CODEX/Phenocycler-Fusion v1 Open
The purpose of this SOP is to outline the techniques for sectioning and storage of fresh-frozen tissue samples for PhenoCycler-Fusion experiments
View article: Supplementary Table S15 from Cross-Species Single-Cell Analysis of Pancreatic Ductal Adenocarcinoma Reveals Antigen-Presenting Cancer-Associated Fibroblasts
Supplementary Table S15 from Cross-Species Single-Cell Analysis of Pancreatic Ductal Adenocarcinoma Reveals Antigen-Presenting Cancer-Associated Fibroblasts Open
Supplementary Table S15 shows protein activity of signaling molecules in human CAFs, as analyzed by VIPER
View article: Supplementary Table S4 from Cross-Species Single-Cell Analysis of Pancreatic Ductal Adenocarcinoma Reveals Antigen-Presenting Cancer-Associated Fibroblasts
Supplementary Table S4 from Cross-Species Single-Cell Analysis of Pancreatic Ductal Adenocarcinoma Reveals Antigen-Presenting Cancer-Associated Fibroblasts Open
Supplementary Table S4 shows marker genes of the different clusters in human PDAC scRNAseq
View article: Supplementary Table S6 from Cross-Species Single-Cell Analysis of Pancreatic Ductal Adenocarcinoma Reveals Antigen-Presenting Cancer-Associated Fibroblasts
Supplementary Table S6 from Cross-Species Single-Cell Analysis of Pancreatic Ductal Adenocarcinoma Reveals Antigen-Presenting Cancer-Associated Fibroblasts Open
Supplementary Table S6 shows marker genes of the different human ductal cell sub-clusters
View article: Supplementary Table S14 from Cross-Species Single-Cell Analysis of Pancreatic Ductal Adenocarcinoma Reveals Antigen-Presenting Cancer-Associated Fibroblasts
Supplementary Table S14 from Cross-Species Single-Cell Analysis of Pancreatic Ductal Adenocarcinoma Reveals Antigen-Presenting Cancer-Associated Fibroblasts Open
Supplementary Table S14 shows GSEA of human PDAC myCAFs vs. iCAFs
View article: Supplementary Table S16 from Cross-Species Single-Cell Analysis of Pancreatic Ductal Adenocarcinoma Reveals Antigen-Presenting Cancer-Associated Fibroblasts
Supplementary Table S16 from Cross-Species Single-Cell Analysis of Pancreatic Ductal Adenocarcinoma Reveals Antigen-Presenting Cancer-Associated Fibroblasts Open
Supplementary Table S16 shows protein activity of transcription factors in human CAFs, as analyzed by VIPER
View article: Supplementary Table S23 from Cross-Species Single-Cell Analysis of Pancreatic Ductal Adenocarcinoma Reveals Antigen-Presenting Cancer-Associated Fibroblasts
Supplementary Table S23 from Cross-Species Single-Cell Analysis of Pancreatic Ductal Adenocarcinoma Reveals Antigen-Presenting Cancer-Associated Fibroblasts Open
Supplementary Table S23 shows GSEA of KPC mouse CAFs
View article: Supplementary Table S4 from Cross-Species Single-Cell Analysis of Pancreatic Ductal Adenocarcinoma Reveals Antigen-Presenting Cancer-Associated Fibroblasts
Supplementary Table S4 from Cross-Species Single-Cell Analysis of Pancreatic Ductal Adenocarcinoma Reveals Antigen-Presenting Cancer-Associated Fibroblasts Open
Supplementary Table S4 shows marker genes of the different clusters in human PDAC scRNAseq
View article: Supplementary Table S15 from Cross-Species Single-Cell Analysis of Pancreatic Ductal Adenocarcinoma Reveals Antigen-Presenting Cancer-Associated Fibroblasts
Supplementary Table S15 from Cross-Species Single-Cell Analysis of Pancreatic Ductal Adenocarcinoma Reveals Antigen-Presenting Cancer-Associated Fibroblasts Open
Supplementary Table S15 shows protein activity of signaling molecules in human CAFs, as analyzed by VIPER
View article: Supplementary Table S22 from Cross-Species Single-Cell Analysis of Pancreatic Ductal Adenocarcinoma Reveals Antigen-Presenting Cancer-Associated Fibroblasts
Supplementary Table S22 from Cross-Species Single-Cell Analysis of Pancreatic Ductal Adenocarcinoma Reveals Antigen-Presenting Cancer-Associated Fibroblasts Open
Supplementary Table S22 shows the marker genes of the different KPC fibroblasts sub-clusters
View article: Supplementary Table S8 from Cross-Species Single-Cell Analysis of Pancreatic Ductal Adenocarcinoma Reveals Antigen-Presenting Cancer-Associated Fibroblasts
Supplementary Table S8 from Cross-Species Single-Cell Analysis of Pancreatic Ductal Adenocarcinoma Reveals Antigen-Presenting Cancer-Associated Fibroblasts Open
Supplementary Table S8 shows marker genes of the different human myeloid cell sub-clusters
View article: Data from Cross-Species Single-Cell Analysis of Pancreatic Ductal Adenocarcinoma Reveals Antigen-Presenting Cancer-Associated Fibroblasts
Data from Cross-Species Single-Cell Analysis of Pancreatic Ductal Adenocarcinoma Reveals Antigen-Presenting Cancer-Associated Fibroblasts Open
Cancer-associated fibroblasts (CAF) are major players in the progression and drug resistance of pancreatic ductal adenocarcinoma (PDAC). CAFs constitute a diverse cell population consisting of several recently described subtypes, although …
View article: Supplementary Table S13 from Cross-Species Single-Cell Analysis of Pancreatic Ductal Adenocarcinoma Reveals Antigen-Presenting Cancer-Associated Fibroblasts
Supplementary Table S13 from Cross-Species Single-Cell Analysis of Pancreatic Ductal Adenocarcinoma Reveals Antigen-Presenting Cancer-Associated Fibroblasts Open
Supplementary Table S13 shows marker genes of the different human fibroblasts
View article: Supplementary Figures S1-S8 from Cross-Species Single-Cell Analysis of Pancreatic Ductal Adenocarcinoma Reveals Antigen-Presenting Cancer-Associated Fibroblasts
Supplementary Figures S1-S8 from Cross-Species Single-Cell Analysis of Pancreatic Ductal Adenocarcinoma Reveals Antigen-Presenting Cancer-Associated Fibroblasts Open
Supplementary Figure S1 shows the data quality and clustering metrics of the human PDAC single cell transcriptomes, Supplementary Figure S2 shows the distribution of sub-clusters of cells throughout the human dataset, Supplementary Figure …
View article: Supplementary Table S22 from Cross-Species Single-Cell Analysis of Pancreatic Ductal Adenocarcinoma Reveals Antigen-Presenting Cancer-Associated Fibroblasts
Supplementary Table S22 from Cross-Species Single-Cell Analysis of Pancreatic Ductal Adenocarcinoma Reveals Antigen-Presenting Cancer-Associated Fibroblasts Open
Supplementary Table S22 shows the marker genes of the different KPC fibroblasts sub-clusters
View article: Supplementary Table S24 from Cross-Species Single-Cell Analysis of Pancreatic Ductal Adenocarcinoma Reveals Antigen-Presenting Cancer-Associated Fibroblasts
Supplementary Table S24 from Cross-Species Single-Cell Analysis of Pancreatic Ductal Adenocarcinoma Reveals Antigen-Presenting Cancer-Associated Fibroblasts Open
Supplementary Table S24 shows VIPER analysis of protein activity in KPC mouse CAFs
View article: Supplementary Table S18 from Cross-Species Single-Cell Analysis of Pancreatic Ductal Adenocarcinoma Reveals Antigen-Presenting Cancer-Associated Fibroblasts
Supplementary Table S18 from Cross-Species Single-Cell Analysis of Pancreatic Ductal Adenocarcinoma Reveals Antigen-Presenting Cancer-Associated Fibroblasts Open
Supplementary Table S18 shows the marker genes of the different clusters in all viable KPC dataset
View article: Supplementary Table S20 from Cross-Species Single-Cell Analysis of Pancreatic Ductal Adenocarcinoma Reveals Antigen-Presenting Cancer-Associated Fibroblasts
Supplementary Table S20 from Cross-Species Single-Cell Analysis of Pancreatic Ductal Adenocarcinoma Reveals Antigen-Presenting Cancer-Associated Fibroblasts Open
Supplementary Table S20 shows the marker genes of the different clusters in the fibroblast-enriched KPC analysis
View article: Supplementary Table S10 from Cross-Species Single-Cell Analysis of Pancreatic Ductal Adenocarcinoma Reveals Antigen-Presenting Cancer-Associated Fibroblasts
Supplementary Table S10 from Cross-Species Single-Cell Analysis of Pancreatic Ductal Adenocarcinoma Reveals Antigen-Presenting Cancer-Associated Fibroblasts Open
Supplementary Table S10 shows marker genes of the different human T & NK cell sub-clusters
View article: Supplementary Table S18 from Cross-Species Single-Cell Analysis of Pancreatic Ductal Adenocarcinoma Reveals Antigen-Presenting Cancer-Associated Fibroblasts
Supplementary Table S18 from Cross-Species Single-Cell Analysis of Pancreatic Ductal Adenocarcinoma Reveals Antigen-Presenting Cancer-Associated Fibroblasts Open
Supplementary Table S18 shows the marker genes of the different clusters in all viable KPC dataset