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a , Patients were randomized to neoadjuvant radiotherapy followed by surgery (control) or 3 cycles of neoadjuvant pembrolizumab and radiotherapy followed by surgery and up to 14 cycles of adjuvant pembrolizumab (experimental). Bulk RNA was isolated from formalin-fixed paraffin embedded <t>(FFPE)</t> pre-treatment tumor biopsies and surgical resection tumor specimens prior to next-generation sequencing and digital cytometry to measure cell state abundances. Fresh surgical resection specimens after preoperative radiotherapy with or without pembrolizumab were dissociated prior to analysis with flow cytometry. Peripheral blood mononuclear cells (PBMCs) were isolated from longitudinal peripheral blood samples for analysis using cytometry by time-of-flight (CyTOF).
Ffpe Pre Treatment Core Needle Biopsies, supplied by Biotium, used in various techniques. Bioz Stars score: 94/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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fresh-frozen pretreatment core needle tumor biopsies  (Novogene)
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a , Patients were randomized to neoadjuvant radiotherapy followed by surgery (control) or 3 cycles of neoadjuvant pembrolizumab and radiotherapy followed by surgery and up to 14 cycles of adjuvant pembrolizumab (experimental). Bulk RNA was isolated from formalin-fixed paraffin embedded <t>(FFPE)</t> pre-treatment tumor biopsies and surgical resection tumor specimens prior to next-generation sequencing and digital cytometry to measure cell state abundances. Fresh surgical resection specimens after preoperative radiotherapy with or without pembrolizumab were dissociated prior to analysis with flow cytometry. Peripheral blood mononuclear cells (PBMCs) were isolated from longitudinal peripheral blood samples for analysis using cytometry by time-of-flight (CyTOF).
Fresh Frozen Pretreatment Core Needle Tumor Biopsies, supplied by Novogene, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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introducer needle and an 18g core biopsy instrument  (Argon Medical Devices Inc)
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a , Patients were randomized to neoadjuvant radiotherapy followed by surgery (control) or 3 cycles of neoadjuvant pembrolizumab and radiotherapy followed by surgery and up to 14 cycles of adjuvant pembrolizumab (experimental). Bulk RNA was isolated from formalin-fixed paraffin embedded <t>(FFPE)</t> pre-treatment tumor biopsies and surgical resection tumor specimens prior to next-generation sequencing and digital cytometry to measure cell state abundances. Fresh surgical resection specimens after preoperative radiotherapy with or without pembrolizumab were dissociated prior to analysis with flow cytometry. Peripheral blood mononuclear cells (PBMCs) were isolated from longitudinal peripheral blood samples for analysis using cytometry by time-of-flight (CyTOF).
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a , Patients were randomized to neoadjuvant radiotherapy followed by surgery (control) or 3 cycles of neoadjuvant pembrolizumab and radiotherapy followed by surgery and up to 14 cycles of adjuvant pembrolizumab (experimental). Bulk RNA was isolated from formalin-fixed paraffin embedded <t>(FFPE)</t> pre-treatment tumor biopsies and surgical resection tumor specimens prior to next-generation sequencing and digital cytometry to measure cell state abundances. Fresh surgical resection specimens after preoperative radiotherapy with or without pembrolizumab were dissociated prior to analysis with flow cytometry. Peripheral blood mononuclear cells (PBMCs) were isolated from longitudinal peripheral blood samples for analysis using cytometry by time-of-flight (CyTOF).
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percutaneous core needle biopsy  (Pohlig GmbH)
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a , Patients were randomized to neoadjuvant radiotherapy followed by surgery (control) or 3 cycles of neoadjuvant pembrolizumab and radiotherapy followed by surgery and up to 14 cycles of adjuvant pembrolizumab (experimental). Bulk RNA was isolated from formalin-fixed paraffin embedded <t>(FFPE)</t> pre-treatment tumor biopsies and surgical resection tumor specimens prior to next-generation sequencing and digital cytometry to measure cell state abundances. Fresh surgical resection specimens after preoperative radiotherapy with or without pembrolizumab were dissociated prior to analysis with flow cytometry. Peripheral blood mononuclear cells (PBMCs) were isolated from longitudinal peripheral blood samples for analysis using cytometry by time-of-flight (CyTOF).
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core needle biopsy  (Diagnos Inc)
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a , Patients were randomized to neoadjuvant radiotherapy followed by surgery (control) or 3 cycles of neoadjuvant pembrolizumab and radiotherapy followed by surgery and up to 14 cycles of adjuvant pembrolizumab (experimental). Bulk RNA was isolated from formalin-fixed paraffin embedded <t>(FFPE)</t> pre-treatment tumor biopsies and surgical resection tumor specimens prior to next-generation sequencing and digital cytometry to measure cell state abundances. Fresh surgical resection specimens after preoperative radiotherapy with or without pembrolizumab were dissociated prior to analysis with flow cytometry. Peripheral blood mononuclear cells (PBMCs) were isolated from longitudinal peripheral blood samples for analysis using cytometry by time-of-flight (CyTOF).
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forward facing biopsy needle quick-core  (Cook Medical Inc)
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a , Patients were randomized to neoadjuvant radiotherapy followed by surgery (control) or 3 cycles of neoadjuvant pembrolizumab and radiotherapy followed by surgery and up to 14 cycles of adjuvant pembrolizumab (experimental). Bulk RNA was isolated from formalin-fixed paraffin embedded <t>(FFPE)</t> pre-treatment tumor biopsies and surgical resection tumor specimens prior to next-generation sequencing and digital cytometry to measure cell state abundances. Fresh surgical resection specimens after preoperative radiotherapy with or without pembrolizumab were dissociated prior to analysis with flow cytometry. Peripheral blood mononuclear cells (PBMCs) were isolated from longitudinal peripheral blood samples for analysis using cytometry by time-of-flight (CyTOF).
Forward Facing Biopsy Needle Quick Core, supplied by Cook Medical Inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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de novo asc diagnosed on core needle biopsy  (Basler)
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Basler de novo asc diagnosed on core needle biopsy
a , Patients were randomized to neoadjuvant radiotherapy followed by surgery (control) or 3 cycles of neoadjuvant pembrolizumab and radiotherapy followed by surgery and up to 14 cycles of adjuvant pembrolizumab (experimental). Bulk RNA was isolated from formalin-fixed paraffin embedded <t>(FFPE)</t> pre-treatment tumor biopsies and surgical resection tumor specimens prior to next-generation sequencing and digital cytometry to measure cell state abundances. Fresh surgical resection specimens after preoperative radiotherapy with or without pembrolizumab were dissociated prior to analysis with flow cytometry. Peripheral blood mononuclear cells (PBMCs) were isolated from longitudinal peripheral blood samples for analysis using cytometry by time-of-flight (CyTOF).
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biopsy needle 18 gauge × biopincetm full core biopsy instrument  (Argon Medical Devices Inc)
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Argon Medical Devices Inc biopsy needle 18 gauge × biopincetm full core biopsy instrument
a , Patients were randomized to neoadjuvant radiotherapy followed by surgery (control) or 3 cycles of neoadjuvant pembrolizumab and radiotherapy followed by surgery and up to 14 cycles of adjuvant pembrolizumab (experimental). Bulk RNA was isolated from formalin-fixed paraffin embedded <t>(FFPE)</t> pre-treatment tumor biopsies and surgical resection tumor specimens prior to next-generation sequencing and digital cytometry to measure cell state abundances. Fresh surgical resection specimens after preoperative radiotherapy with or without pembrolizumab were dissociated prior to analysis with flow cytometry. Peripheral blood mononuclear cells (PBMCs) were isolated from longitudinal peripheral blood samples for analysis using cytometry by time-of-flight (CyTOF).
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image‐guided core needle biopsies  (Johns Hopkins HealthCare)
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Johns Hopkins HealthCare image‐guided core needle biopsies
a , Patients were randomized to neoadjuvant radiotherapy followed by surgery (control) or 3 cycles of neoadjuvant pembrolizumab and radiotherapy followed by surgery and up to 14 cycles of adjuvant pembrolizumab (experimental). Bulk RNA was isolated from formalin-fixed paraffin embedded <t>(FFPE)</t> pre-treatment tumor biopsies and surgical resection tumor specimens prior to next-generation sequencing and digital cytometry to measure cell state abundances. Fresh surgical resection specimens after preoperative radiotherapy with or without pembrolizumab were dissociated prior to analysis with flow cytometry. Peripheral blood mononuclear cells (PBMCs) were isolated from longitudinal peripheral blood samples for analysis using cytometry by time-of-flight (CyTOF).
Image‐Guided Core Needle Biopsies, supplied by Johns Hopkins HealthCare, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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Image Search Results


a , Patients were randomized to neoadjuvant radiotherapy followed by surgery (control) or 3 cycles of neoadjuvant pembrolizumab and radiotherapy followed by surgery and up to 14 cycles of adjuvant pembrolizumab (experimental). Bulk RNA was isolated from formalin-fixed paraffin embedded (FFPE) pre-treatment tumor biopsies and surgical resection tumor specimens prior to next-generation sequencing and digital cytometry to measure cell state abundances. Fresh surgical resection specimens after preoperative radiotherapy with or without pembrolizumab were dissociated prior to analysis with flow cytometry. Peripheral blood mononuclear cells (PBMCs) were isolated from longitudinal peripheral blood samples for analysis using cytometry by time-of-flight (CyTOF).

Journal: medRxiv

Article Title: Distinct Sarcoma Microenvironments Predict Benefit from Addition of Pembrolizumab to Preoperative Radiotherapy and Surgery in SU2C-SARC032

doi: 10.1101/2025.11.01.25339299

Figure Lengend Snippet: a , Patients were randomized to neoadjuvant radiotherapy followed by surgery (control) or 3 cycles of neoadjuvant pembrolizumab and radiotherapy followed by surgery and up to 14 cycles of adjuvant pembrolizumab (experimental). Bulk RNA was isolated from formalin-fixed paraffin embedded (FFPE) pre-treatment tumor biopsies and surgical resection tumor specimens prior to next-generation sequencing and digital cytometry to measure cell state abundances. Fresh surgical resection specimens after preoperative radiotherapy with or without pembrolizumab were dissociated prior to analysis with flow cytometry. Peripheral blood mononuclear cells (PBMCs) were isolated from longitudinal peripheral blood samples for analysis using cytometry by time-of-flight (CyTOF).

Article Snippet: RNA was extracted from FFPE pre-treatment core needle biopsies and surgically resected tumors using RNAstorm FFPE RNA Extraction Kits (Cell Data Sciences).

Techniques: Control, Adjuvant, Isolation, Formalin-fixed Paraffin-Embedded, Next-Generation Sequencing, Cytometry, Flow Cytometry

a , UMAP plots showing the different non-malignant and malignant cell states identified for each major cell type in the STS scRNA-seq reference atlas, including endothelial cells, cancer associated fibroblasts (CAFs), B cells, lymphoid, and myeloid cells. b , Scatter plots showing the correlation between the abundance of cell types recovered in bulk RNA-seq of post-treatment formalin-fixed paraffin embedded (FFPE) samples using CIBERSORTx and measured through flow cytometry in the matched dissociated fresh tumor samples. Spearman’s correlation coefficients and two-sided P-values are displayed on the graph. The line of best fit by linear regression and 95% confidence intervals are shown on the graph.

Journal: medRxiv

Article Title: Distinct Sarcoma Microenvironments Predict Benefit from Addition of Pembrolizumab to Preoperative Radiotherapy and Surgery in SU2C-SARC032

doi: 10.1101/2025.11.01.25339299

Figure Lengend Snippet: a , UMAP plots showing the different non-malignant and malignant cell states identified for each major cell type in the STS scRNA-seq reference atlas, including endothelial cells, cancer associated fibroblasts (CAFs), B cells, lymphoid, and myeloid cells. b , Scatter plots showing the correlation between the abundance of cell types recovered in bulk RNA-seq of post-treatment formalin-fixed paraffin embedded (FFPE) samples using CIBERSORTx and measured through flow cytometry in the matched dissociated fresh tumor samples. Spearman’s correlation coefficients and two-sided P-values are displayed on the graph. The line of best fit by linear regression and 95% confidence intervals are shown on the graph.

Article Snippet: RNA was extracted from FFPE pre-treatment core needle biopsies and surgically resected tumors using RNAstorm FFPE RNA Extraction Kits (Cell Data Sciences).

Techniques: RNA Sequencing, Formalin-fixed Paraffin-Embedded, Flow Cytometry