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Structured Review

10X Genomics cellranger version 6.0.0 software
Cellranger Version 6.0.0 Software, supplied by 10X Genomics, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/cellranger+version+6%2E0%2E0/cellranger/pmc11979601__jitc___13___4___s002-28-13-11
Average 90 stars, based on 1 article reviews
cellranger version 6.0.0 software - by Bioz Stars, 2026-09
90/100 stars

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Related Articles

Recombinant:

Article Title: Excess pancreatic elastase alters acinar-to-β-cell communication by impairing the mechano-signaling and the PAR2 pathways
Article Snippet: Cellranger version 6.0.0 , 10x Genomics , https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/latest;RRID:SCR_017344.

Article Title: Single-cell RNA sequencing reveals the suppressive effect of PPP1R15A inhibitor Sephin1 in antitumor immunity
Article Snippet: CellRanger , 10X Genomics , Version 6.0.0.

Article Title: Cell-cell interactome of the hematopoietic niche and its changes in acute myeloid leukemia
Article Snippet: CellRanger version 6.0.0 , 10X Genomics , https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/installation.

Article Title: Developmental changes and metabolic reprogramming during establishment of infection and progression of Trypanosoma brucei brucei through its insect host
Article Snippet: Moreover, using Cellranger version 6.0.0 (10x Genomics), the percentage of reads assigned to the transcriptome increased from 41% to 48.5%, and the number of reads assigned to intergenic regions decreased from 14.5% to 4.4% compared to the GTF file generated from the current GFF file from TriTrypDB.

Article Title: Single-cell transcriptomic and spatial landscapes of the developing human pancreas.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Critical commercial assays 10x Chromium Single Cell 30 GEM, Library & Gel Bead Kit v3.1 10x Genomics Cat#1000269 Visium Spatial Gene Expression Slide & Reagent Kit 10x Genomics Cat#1000184 Agilent RNA 6000 Pico Reagents Agilent Technologies Cat# 5067-1513 Visium Spatial tissue optimization kit 10x Genomics Cat#1000191 Visium accessory kit 10x Genomics Cat#1000194 Deposited data Dataset generated from a different study https://ngdc.cncb.ac.cn/omix OMIX: OMIX236 Single cell RNA-Seq data generated in this study https://www.ncbi.nlm.nih.gov/geo/ GEO: GSE197064 Spatial transcriptomics data generated in this study https://www.ncbi.nlm.nih.gov/geo/ GEO: GSE197317 Software and algorithms Cellranger version 6.0.0 10x Genomics https://support.10xgenomics.com/single-cell- gene-expression/software/downloads/latest Spaceranger version 3.1.0 10x Genomics https://support.10xgenomics.com/single-cell- gene-expression/software/downloads/latest Giotto version 1.0.3 Github, Dries et al.30 https://rubd.github.io/Giotto_site/ Seurat version 4.0.6 R CRAN https://satijalab.org/seurat/ Monocle version 3 R Bioconductor https://cole-trapnell-lab.github.io/monocle3/ stLearn Github; Pham et al.35 https://github.com/BiomedicalMachineLearning/ stLearn slingshot 2.5.2 Street et al.40 https://github.com/kstreet13/slingshot


Software:

Article Title: Excess pancreatic elastase alters acinar-to-β-cell communication by impairing the mechano-signaling and the PAR2 pathways
Article Snippet: Cellranger version 6.0.0 , 10x Genomics , https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/latest;RRID:SCR_017344.

Article Title: Single-cell RNA sequencing reveals the suppressive effect of PPP1R15A inhibitor Sephin1 in antitumor immunity
Article Snippet: CellRanger , 10X Genomics , Version 6.0.0.

Article Title: Cell-cell interactome of the hematopoietic niche and its changes in acute myeloid leukemia
Article Snippet: CellRanger version 6.0.0 , 10X Genomics , https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/installation.

Article Title: Developmental changes and metabolic reprogramming during establishment of infection and progression of Trypanosoma brucei brucei through its insect host
Article Snippet: Moreover, using Cellranger version 6.0.0 (10x Genomics), the percentage of reads assigned to the transcriptome increased from 41% to 48.5%, and the number of reads assigned to intergenic regions decreased from 14.5% to 4.4% compared to the GTF file generated from the current GFF file from TriTrypDB.

Article Title: Single-cell transcriptomic and spatial landscapes of the developing human pancreas.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Critical commercial assays 10x Chromium Single Cell 30 GEM, Library & Gel Bead Kit v3.1 10x Genomics Cat#1000269 Visium Spatial Gene Expression Slide & Reagent Kit 10x Genomics Cat#1000184 Agilent RNA 6000 Pico Reagents Agilent Technologies Cat# 5067-1513 Visium Spatial tissue optimization kit 10x Genomics Cat#1000191 Visium accessory kit 10x Genomics Cat#1000194 Deposited data Dataset generated from a different study https://ngdc.cncb.ac.cn/omix OMIX: OMIX236 Single cell RNA-Seq data generated in this study https://www.ncbi.nlm.nih.gov/geo/ GEO: GSE197064 Spatial transcriptomics data generated in this study https://www.ncbi.nlm.nih.gov/geo/ GEO: GSE197317 Software and algorithms Cellranger version 6.0.0 10x Genomics https://support.10xgenomics.com/single-cell- gene-expression/software/downloads/latest Spaceranger version 3.1.0 10x Genomics https://support.10xgenomics.com/single-cell- gene-expression/software/downloads/latest Giotto version 1.0.3 Github, Dries et al.30 https://rubd.github.io/Giotto_site/ Seurat version 4.0.6 R CRAN https://satijalab.org/seurat/ Monocle version 3 R Bioconductor https://cole-trapnell-lab.github.io/monocle3/ stLearn Github; Pham et al.35 https://github.com/BiomedicalMachineLearning/ stLearn slingshot 2.5.2 Street et al.40 https://github.com/kstreet13/slingshot


Expressing:

Article Title: Excess pancreatic elastase alters acinar-to-β-cell communication by impairing the mechano-signaling and the PAR2 pathways
Article Snippet: Cellranger version 6.0.0 , 10x Genomics , https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/latest;RRID:SCR_017344.

Article Title: Single-cell RNA sequencing reveals the suppressive effect of PPP1R15A inhibitor Sephin1 in antitumor immunity
Article Snippet: CellRanger , 10X Genomics , Version 6.0.0.

Article Title: Cell-cell interactome of the hematopoietic niche and its changes in acute myeloid leukemia
Article Snippet: CellRanger version 6.0.0 , 10X Genomics , https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/installation.

Article Title: Developmental changes and metabolic reprogramming during establishment of infection and progression of Trypanosoma brucei brucei through its insect host
Article Snippet: Moreover, using Cellranger version 6.0.0 (10x Genomics), the percentage of reads assigned to the transcriptome increased from 41% to 48.5%, and the number of reads assigned to intergenic regions decreased from 14.5% to 4.4% compared to the GTF file generated from the current GFF file from TriTrypDB.

Article Title: Single-cell transcriptomic and spatial landscapes of the developing human pancreas.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Critical commercial assays 10x Chromium Single Cell 30 GEM, Library & Gel Bead Kit v3.1 10x Genomics Cat#1000269 Visium Spatial Gene Expression Slide & Reagent Kit 10x Genomics Cat#1000184 Agilent RNA 6000 Pico Reagents Agilent Technologies Cat# 5067-1513 Visium Spatial tissue optimization kit 10x Genomics Cat#1000191 Visium accessory kit 10x Genomics Cat#1000194 Deposited data Dataset generated from a different study https://ngdc.cncb.ac.cn/omix OMIX: OMIX236 Single cell RNA-Seq data generated in this study https://www.ncbi.nlm.nih.gov/geo/ GEO: GSE197064 Spatial transcriptomics data generated in this study https://www.ncbi.nlm.nih.gov/geo/ GEO: GSE197317 Software and algorithms Cellranger version 6.0.0 10x Genomics https://support.10xgenomics.com/single-cell- gene-expression/software/downloads/latest Spaceranger version 3.1.0 10x Genomics https://support.10xgenomics.com/single-cell- gene-expression/software/downloads/latest Giotto version 1.0.3 Github, Dries et al.30 https://rubd.github.io/Giotto_site/ Seurat version 4.0.6 R CRAN https://satijalab.org/seurat/ Monocle version 3 R Bioconductor https://cole-trapnell-lab.github.io/monocle3/ stLearn Github; Pham et al.35 https://github.com/BiomedicalMachineLearning/ stLearn slingshot 2.5.2 Street et al.40 https://github.com/kstreet13/slingshot


Transfection:

Article Title: Excess pancreatic elastase alters acinar-to-β-cell communication by impairing the mechano-signaling and the PAR2 pathways
Article Snippet: Cellranger version 6.0.0 , 10x Genomics , https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/latest;RRID:SCR_017344.

Article Title: Single-cell RNA sequencing reveals the suppressive effect of PPP1R15A inhibitor Sephin1 in antitumor immunity
Article Snippet: CellRanger , 10X Genomics , Version 6.0.0.

Article Title: Cell-cell interactome of the hematopoietic niche and its changes in acute myeloid leukemia
Article Snippet: CellRanger version 6.0.0 , 10X Genomics , https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/installation.

Article Title: Developmental changes and metabolic reprogramming during establishment of infection and progression of Trypanosoma brucei brucei through its insect host
Article Snippet: Moreover, using Cellranger version 6.0.0 (10x Genomics), the percentage of reads assigned to the transcriptome increased from 41% to 48.5%, and the number of reads assigned to intergenic regions decreased from 14.5% to 4.4% compared to the GTF file generated from the current GFF file from TriTrypDB.

Article Title: Single-cell transcriptomic and spatial landscapes of the developing human pancreas.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Critical commercial assays 10x Chromium Single Cell 30 GEM, Library & Gel Bead Kit v3.1 10x Genomics Cat#1000269 Visium Spatial Gene Expression Slide & Reagent Kit 10x Genomics Cat#1000184 Agilent RNA 6000 Pico Reagents Agilent Technologies Cat# 5067-1513 Visium Spatial tissue optimization kit 10x Genomics Cat#1000191 Visium accessory kit 10x Genomics Cat#1000194 Deposited data Dataset generated from a different study https://ngdc.cncb.ac.cn/omix OMIX: OMIX236 Single cell RNA-Seq data generated in this study https://www.ncbi.nlm.nih.gov/geo/ GEO: GSE197064 Spatial transcriptomics data generated in this study https://www.ncbi.nlm.nih.gov/geo/ GEO: GSE197317 Software and algorithms Cellranger version 6.0.0 10x Genomics https://support.10xgenomics.com/single-cell- gene-expression/software/downloads/latest Spaceranger version 3.1.0 10x Genomics https://support.10xgenomics.com/single-cell- gene-expression/software/downloads/latest Giotto version 1.0.3 Github, Dries et al.30 https://rubd.github.io/Giotto_site/ Seurat version 4.0.6 R CRAN https://satijalab.org/seurat/ Monocle version 3 R Bioconductor https://cole-trapnell-lab.github.io/monocle3/ stLearn Github; Pham et al.35 https://github.com/BiomedicalMachineLearning/ stLearn slingshot 2.5.2 Street et al.40 https://github.com/kstreet13/slingshot


Binding Assay:

Article Title: Excess pancreatic elastase alters acinar-to-β-cell communication by impairing the mechano-signaling and the PAR2 pathways
Article Snippet: Cellranger version 6.0.0 , 10x Genomics , https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/latest;RRID:SCR_017344.

Article Title: Single-cell RNA sequencing reveals the suppressive effect of PPP1R15A inhibitor Sephin1 in antitumor immunity
Article Snippet: CellRanger , 10X Genomics , Version 6.0.0.

Article Title: Cell-cell interactome of the hematopoietic niche and its changes in acute myeloid leukemia
Article Snippet: CellRanger version 6.0.0 , 10X Genomics , https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/installation.

Article Title: Developmental changes and metabolic reprogramming during establishment of infection and progression of Trypanosoma brucei brucei through its insect host
Article Snippet: Moreover, using Cellranger version 6.0.0 (10x Genomics), the percentage of reads assigned to the transcriptome increased from 41% to 48.5%, and the number of reads assigned to intergenic regions decreased from 14.5% to 4.4% compared to the GTF file generated from the current GFF file from TriTrypDB.

Article Title: Single-cell transcriptomic and spatial landscapes of the developing human pancreas.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Critical commercial assays 10x Chromium Single Cell 30 GEM, Library & Gel Bead Kit v3.1 10x Genomics Cat#1000269 Visium Spatial Gene Expression Slide & Reagent Kit 10x Genomics Cat#1000184 Agilent RNA 6000 Pico Reagents Agilent Technologies Cat# 5067-1513 Visium Spatial tissue optimization kit 10x Genomics Cat#1000191 Visium accessory kit 10x Genomics Cat#1000194 Deposited data Dataset generated from a different study https://ngdc.cncb.ac.cn/omix OMIX: OMIX236 Single cell RNA-Seq data generated in this study https://www.ncbi.nlm.nih.gov/geo/ GEO: GSE197064 Spatial transcriptomics data generated in this study https://www.ncbi.nlm.nih.gov/geo/ GEO: GSE197317 Software and algorithms Cellranger version 6.0.0 10x Genomics https://support.10xgenomics.com/single-cell- gene-expression/software/downloads/latest Spaceranger version 3.1.0 10x Genomics https://support.10xgenomics.com/single-cell- gene-expression/software/downloads/latest Giotto version 1.0.3 Github, Dries et al.30 https://rubd.github.io/Giotto_site/ Seurat version 4.0.6 R CRAN https://satijalab.org/seurat/ Monocle version 3 R Bioconductor https://cole-trapnell-lab.github.io/monocle3/ stLearn Github; Pham et al.35 https://github.com/BiomedicalMachineLearning/ stLearn slingshot 2.5.2 Street et al.40 https://github.com/kstreet13/slingshot


Fat:

Article Title: Excess pancreatic elastase alters acinar-to-β-cell communication by impairing the mechano-signaling and the PAR2 pathways
Article Snippet: Cellranger version 6.0.0 , 10x Genomics , https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/latest;RRID:SCR_017344.

Article Title: Single-cell RNA sequencing reveals the suppressive effect of PPP1R15A inhibitor Sephin1 in antitumor immunity
Article Snippet: CellRanger , 10X Genomics , Version 6.0.0.

Article Title: Cell-cell interactome of the hematopoietic niche and its changes in acute myeloid leukemia
Article Snippet: CellRanger version 6.0.0 , 10X Genomics , https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/installation.

Article Title: Developmental changes and metabolic reprogramming during establishment of infection and progression of Trypanosoma brucei brucei through its insect host
Article Snippet: Moreover, using Cellranger version 6.0.0 (10x Genomics), the percentage of reads assigned to the transcriptome increased from 41% to 48.5%, and the number of reads assigned to intergenic regions decreased from 14.5% to 4.4% compared to the GTF file generated from the current GFF file from TriTrypDB.

Article Title: Single-cell transcriptomic and spatial landscapes of the developing human pancreas.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Critical commercial assays 10x Chromium Single Cell 30 GEM, Library & Gel Bead Kit v3.1 10x Genomics Cat#1000269 Visium Spatial Gene Expression Slide & Reagent Kit 10x Genomics Cat#1000184 Agilent RNA 6000 Pico Reagents Agilent Technologies Cat# 5067-1513 Visium Spatial tissue optimization kit 10x Genomics Cat#1000191 Visium accessory kit 10x Genomics Cat#1000194 Deposited data Dataset generated from a different study https://ngdc.cncb.ac.cn/omix OMIX: OMIX236 Single cell RNA-Seq data generated in this study https://www.ncbi.nlm.nih.gov/geo/ GEO: GSE197064 Spatial transcriptomics data generated in this study https://www.ncbi.nlm.nih.gov/geo/ GEO: GSE197317 Software and algorithms Cellranger version 6.0.0 10x Genomics https://support.10xgenomics.com/single-cell- gene-expression/software/downloads/latest Spaceranger version 3.1.0 10x Genomics https://support.10xgenomics.com/single-cell- gene-expression/software/downloads/latest Giotto version 1.0.3 Github, Dries et al.30 https://rubd.github.io/Giotto_site/ Seurat version 4.0.6 R CRAN https://satijalab.org/seurat/ Monocle version 3 R Bioconductor https://cole-trapnell-lab.github.io/monocle3/ stLearn Github; Pham et al.35 https://github.com/BiomedicalMachineLearning/ stLearn slingshot 2.5.2 Street et al.40 https://github.com/kstreet13/slingshot


Virus:

Article Title: Excess pancreatic elastase alters acinar-to-β-cell communication by impairing the mechano-signaling and the PAR2 pathways
Article Snippet: Cellranger version 6.0.0 , 10x Genomics , https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/latest;RRID:SCR_017344.

Article Title: Single-cell RNA sequencing reveals the suppressive effect of PPP1R15A inhibitor Sephin1 in antitumor immunity
Article Snippet: CellRanger , 10X Genomics , Version 6.0.0.

Article Title: Cell-cell interactome of the hematopoietic niche and its changes in acute myeloid leukemia
Article Snippet: CellRanger version 6.0.0 , 10X Genomics , https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/installation.

Article Title: Developmental changes and metabolic reprogramming during establishment of infection and progression of Trypanosoma brucei brucei through its insect host
Article Snippet: Moreover, using Cellranger version 6.0.0 (10x Genomics), the percentage of reads assigned to the transcriptome increased from 41% to 48.5%, and the number of reads assigned to intergenic regions decreased from 14.5% to 4.4% compared to the GTF file generated from the current GFF file from TriTrypDB.

Article Title: Single-cell transcriptomic and spatial landscapes of the developing human pancreas.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Critical commercial assays 10x Chromium Single Cell 30 GEM, Library & Gel Bead Kit v3.1 10x Genomics Cat#1000269 Visium Spatial Gene Expression Slide & Reagent Kit 10x Genomics Cat#1000184 Agilent RNA 6000 Pico Reagents Agilent Technologies Cat# 5067-1513 Visium Spatial tissue optimization kit 10x Genomics Cat#1000191 Visium accessory kit 10x Genomics Cat#1000194 Deposited data Dataset generated from a different study https://ngdc.cncb.ac.cn/omix OMIX: OMIX236 Single cell RNA-Seq data generated in this study https://www.ncbi.nlm.nih.gov/geo/ GEO: GSE197064 Spatial transcriptomics data generated in this study https://www.ncbi.nlm.nih.gov/geo/ GEO: GSE197317 Software and algorithms Cellranger version 6.0.0 10x Genomics https://support.10xgenomics.com/single-cell- gene-expression/software/downloads/latest Spaceranger version 3.1.0 10x Genomics https://support.10xgenomics.com/single-cell- gene-expression/software/downloads/latest Giotto version 1.0.3 Github, Dries et al.30 https://rubd.github.io/Giotto_site/ Seurat version 4.0.6 R CRAN https://satijalab.org/seurat/ Monocle version 3 R Bioconductor https://cole-trapnell-lab.github.io/monocle3/ stLearn Github; Pham et al.35 https://github.com/BiomedicalMachineLearning/ stLearn slingshot 2.5.2 Street et al.40 https://github.com/kstreet13/slingshot


Activation Assay:

Article Title: Excess pancreatic elastase alters acinar-to-β-cell communication by impairing the mechano-signaling and the PAR2 pathways
Article Snippet: Cellranger version 6.0.0 , 10x Genomics , https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/latest;RRID:SCR_017344.

Article Title: Single-cell RNA sequencing reveals the suppressive effect of PPP1R15A inhibitor Sephin1 in antitumor immunity
Article Snippet: CellRanger , 10X Genomics , Version 6.0.0.

Article Title: Cell-cell interactome of the hematopoietic niche and its changes in acute myeloid leukemia
Article Snippet: CellRanger version 6.0.0 , 10X Genomics , https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/installation.

Article Title: Developmental changes and metabolic reprogramming during establishment of infection and progression of Trypanosoma brucei brucei through its insect host
Article Snippet: Moreover, using Cellranger version 6.0.0 (10x Genomics), the percentage of reads assigned to the transcriptome increased from 41% to 48.5%, and the number of reads assigned to intergenic regions decreased from 14.5% to 4.4% compared to the GTF file generated from the current GFF file from TriTrypDB.

Article Title: Single-cell transcriptomic and spatial landscapes of the developing human pancreas.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Critical commercial assays 10x Chromium Single Cell 30 GEM, Library & Gel Bead Kit v3.1 10x Genomics Cat#1000269 Visium Spatial Gene Expression Slide & Reagent Kit 10x Genomics Cat#1000184 Agilent RNA 6000 Pico Reagents Agilent Technologies Cat# 5067-1513 Visium Spatial tissue optimization kit 10x Genomics Cat#1000191 Visium accessory kit 10x Genomics Cat#1000194 Deposited data Dataset generated from a different study https://ngdc.cncb.ac.cn/omix OMIX: OMIX236 Single cell RNA-Seq data generated in this study https://www.ncbi.nlm.nih.gov/geo/ GEO: GSE197064 Spatial transcriptomics data generated in this study https://www.ncbi.nlm.nih.gov/geo/ GEO: GSE197317 Software and algorithms Cellranger version 6.0.0 10x Genomics https://support.10xgenomics.com/single-cell- gene-expression/software/downloads/latest Spaceranger version 3.1.0 10x Genomics https://support.10xgenomics.com/single-cell- gene-expression/software/downloads/latest Giotto version 1.0.3 Github, Dries et al.30 https://rubd.github.io/Giotto_site/ Seurat version 4.0.6 R CRAN https://satijalab.org/seurat/ Monocle version 3 R Bioconductor https://cole-trapnell-lab.github.io/monocle3/ stLearn Github; Pham et al.35 https://github.com/BiomedicalMachineLearning/ stLearn slingshot 2.5.2 Street et al.40 https://github.com/kstreet13/slingshot


Cell Isolation:

Article Title: Excess pancreatic elastase alters acinar-to-β-cell communication by impairing the mechano-signaling and the PAR2 pathways
Article Snippet: Cellranger version 6.0.0 , 10x Genomics , https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/latest;RRID:SCR_017344.

Article Title: Single-cell RNA sequencing reveals the suppressive effect of PPP1R15A inhibitor Sephin1 in antitumor immunity
Article Snippet: CellRanger , 10X Genomics , Version 6.0.0.

Article Title: Cell-cell interactome of the hematopoietic niche and its changes in acute myeloid leukemia
Article Snippet: CellRanger version 6.0.0 , 10X Genomics , https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/installation.

Article Title: Developmental changes and metabolic reprogramming during establishment of infection and progression of Trypanosoma brucei brucei through its insect host
Article Snippet: Moreover, using Cellranger version 6.0.0 (10x Genomics), the percentage of reads assigned to the transcriptome increased from 41% to 48.5%, and the number of reads assigned to intergenic regions decreased from 14.5% to 4.4% compared to the GTF file generated from the current GFF file from TriTrypDB.

Article Title: Single-cell transcriptomic and spatial landscapes of the developing human pancreas.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Critical commercial assays 10x Chromium Single Cell 30 GEM, Library & Gel Bead Kit v3.1 10x Genomics Cat#1000269 Visium Spatial Gene Expression Slide & Reagent Kit 10x Genomics Cat#1000184 Agilent RNA 6000 Pico Reagents Agilent Technologies Cat# 5067-1513 Visium Spatial tissue optimization kit 10x Genomics Cat#1000191 Visium accessory kit 10x Genomics Cat#1000194 Deposited data Dataset generated from a different study https://ngdc.cncb.ac.cn/omix OMIX: OMIX236 Single cell RNA-Seq data generated in this study https://www.ncbi.nlm.nih.gov/geo/ GEO: GSE197064 Spatial transcriptomics data generated in this study https://www.ncbi.nlm.nih.gov/geo/ GEO: GSE197317 Software and algorithms Cellranger version 6.0.0 10x Genomics https://support.10xgenomics.com/single-cell- gene-expression/software/downloads/latest Spaceranger version 3.1.0 10x Genomics https://support.10xgenomics.com/single-cell- gene-expression/software/downloads/latest Giotto version 1.0.3 Github, Dries et al.30 https://rubd.github.io/Giotto_site/ Seurat version 4.0.6 R CRAN https://satijalab.org/seurat/ Monocle version 3 R Bioconductor https://cole-trapnell-lab.github.io/monocle3/ stLearn Github; Pham et al.35 https://github.com/BiomedicalMachineLearning/ stLearn slingshot 2.5.2 Street et al.40 https://github.com/kstreet13/slingshot


Staining:

Article Title: Excess pancreatic elastase alters acinar-to-β-cell communication by impairing the mechano-signaling and the PAR2 pathways
Article Snippet: Cellranger version 6.0.0 , 10x Genomics , https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/latest;RRID:SCR_017344.

Article Title: Single-cell RNA sequencing reveals the suppressive effect of PPP1R15A inhibitor Sephin1 in antitumor immunity
Article Snippet: CellRanger , 10X Genomics , Version 6.0.0.

Article Title: Cell-cell interactome of the hematopoietic niche and its changes in acute myeloid leukemia
Article Snippet: CellRanger version 6.0.0 , 10X Genomics , https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/installation.

Article Title: Developmental changes and metabolic reprogramming during establishment of infection and progression of Trypanosoma brucei brucei through its insect host
Article Snippet: Moreover, using Cellranger version 6.0.0 (10x Genomics), the percentage of reads assigned to the transcriptome increased from 41% to 48.5%, and the number of reads assigned to intergenic regions decreased from 14.5% to 4.4% compared to the GTF file generated from the current GFF file from TriTrypDB.

Article Title: Single-cell transcriptomic and spatial landscapes of the developing human pancreas.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Critical commercial assays 10x Chromium Single Cell 30 GEM, Library & Gel Bead Kit v3.1 10x Genomics Cat#1000269 Visium Spatial Gene Expression Slide & Reagent Kit 10x Genomics Cat#1000184 Agilent RNA 6000 Pico Reagents Agilent Technologies Cat# 5067-1513 Visium Spatial tissue optimization kit 10x Genomics Cat#1000191 Visium accessory kit 10x Genomics Cat#1000194 Deposited data Dataset generated from a different study https://ngdc.cncb.ac.cn/omix OMIX: OMIX236 Single cell RNA-Seq data generated in this study https://www.ncbi.nlm.nih.gov/geo/ GEO: GSE197064 Spatial transcriptomics data generated in this study https://www.ncbi.nlm.nih.gov/geo/ GEO: GSE197317 Software and algorithms Cellranger version 6.0.0 10x Genomics https://support.10xgenomics.com/single-cell- gene-expression/software/downloads/latest Spaceranger version 3.1.0 10x Genomics https://support.10xgenomics.com/single-cell- gene-expression/software/downloads/latest Giotto version 1.0.3 Github, Dries et al.30 https://rubd.github.io/Giotto_site/ Seurat version 4.0.6 R CRAN https://satijalab.org/seurat/ Monocle version 3 R Bioconductor https://cole-trapnell-lab.github.io/monocle3/ stLearn Github; Pham et al.35 https://github.com/BiomedicalMachineLearning/ stLearn slingshot 2.5.2 Street et al.40 https://github.com/kstreet13/slingshot


Generated:

Article Title: Excess pancreatic elastase alters acinar-to-β-cell communication by impairing the mechano-signaling and the PAR2 pathways
Article Snippet: Cellranger version 6.0.0 , 10x Genomics , https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/latest;RRID:SCR_017344.

Article Title: Single-cell RNA sequencing reveals the suppressive effect of PPP1R15A inhibitor Sephin1 in antitumor immunity
Article Snippet: CellRanger , 10X Genomics , Version 6.0.0.

Article Title: Cell-cell interactome of the hematopoietic niche and its changes in acute myeloid leukemia
Article Snippet: CellRanger version 6.0.0 , 10X Genomics , https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/installation.

Article Title: Developmental changes and metabolic reprogramming during establishment of infection and progression of Trypanosoma brucei brucei through its insect host
Article Snippet: Moreover, using Cellranger version 6.0.0 (10x Genomics), the percentage of reads assigned to the transcriptome increased from 41% to 48.5%, and the number of reads assigned to intergenic regions decreased from 14.5% to 4.4% compared to the GTF file generated from the current GFF file from TriTrypDB.

Article Title: Single-cell transcriptomic and spatial landscapes of the developing human pancreas.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Critical commercial assays 10x Chromium Single Cell 30 GEM, Library & Gel Bead Kit v3.1 10x Genomics Cat#1000269 Visium Spatial Gene Expression Slide & Reagent Kit 10x Genomics Cat#1000184 Agilent RNA 6000 Pico Reagents Agilent Technologies Cat# 5067-1513 Visium Spatial tissue optimization kit 10x Genomics Cat#1000191 Visium accessory kit 10x Genomics Cat#1000194 Deposited data Dataset generated from a different study https://ngdc.cncb.ac.cn/omix OMIX: OMIX236 Single cell RNA-Seq data generated in this study https://www.ncbi.nlm.nih.gov/geo/ GEO: GSE197064 Spatial transcriptomics data generated in this study https://www.ncbi.nlm.nih.gov/geo/ GEO: GSE197317 Software and algorithms Cellranger version 6.0.0 10x Genomics https://support.10xgenomics.com/single-cell- gene-expression/software/downloads/latest Spaceranger version 3.1.0 10x Genomics https://support.10xgenomics.com/single-cell- gene-expression/software/downloads/latest Giotto version 1.0.3 Github, Dries et al.30 https://rubd.github.io/Giotto_site/ Seurat version 4.0.6 R CRAN https://satijalab.org/seurat/ Monocle version 3 R Bioconductor https://cole-trapnell-lab.github.io/monocle3/ stLearn Github; Pham et al.35 https://github.com/BiomedicalMachineLearning/ stLearn slingshot 2.5.2 Street et al.40 https://github.com/kstreet13/slingshot




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