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single index kit n set a  (10X Genomics)

 
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    10X Genomics single index kit n set a
    Single Index Kit N Set A, supplied by 10X Genomics, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/single+index+kit+n+set/a+index+kit+set+single+t/pmc13138057-8-0-7
    Average 86 stars, based on 1 article reviews
    single index kit n set a - by Bioz Stars, 2026-11
    86/100 stars

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    Related Articles

    Single Cell:

    Article Title: Heart tube morphogenesis is regulated by segment-specific gene regulatory networks controlled by MEF2C
    Article Snippet: At this stage, the manufacturer’s protocol for Nuclei Isolation for Single Cell Multiome ATAC + Gene Expression Sequencing, Appendix, Low Cell Input Nuclei Isolation (10x Genomics, CG000365 Rev B) was followed exactly to prepare nuclei for library generation. .. Libraries for snRNA-seq and snATAC-seq were prepared according to the manufacturer’s protocol for Chromium Next GEM Single Cell Multiome ATAC + Gene Expression (10x Genomics, CG000338 Rev B), using the 10x Genomics Chromium controller, Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Bundle (10x Genomics, PN-1000283), Chromium Next GEM Chip J Single Cell Kit (10x Genomics, PN-1000234), Single Index Kit N Set A (10x Genomics, PN-1000212), and Dual Index Kit TT Set A (10x Genomics, PN-1000215). ..


    Article Title: Single-cell multiomic analysis reveals the involvement of Type I interferon-responsive CD8+ T cells in amyloid beta-associated memory loss
    Article Snippet: ∼20K cells per sample were used for preparation of the nuclei for the Assay for Transposase-Accessible Chromatin (ATAC) and gene expression libraries using the low cell input nuclei isolation protocol (10x Genomics). .. The Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Bundle (10x Genomics, #1000283), Chromium Next GEM Chip J Single Cell (10x Genomics, #1000234), Dual Index Kit TT Set A (10x Genomics, #1000215), Single Index Kit N Set A (10x Genomics, #1000212) and Chromium Controller were used according to the manufacturer’s protocols. .. For the ATAC library, a sequencing depth of 25K read pairs per nucleus was used with 50bp paired-end reads using NovaSeq or NextSeq (Illumina).

    Gene Expression:

    Article Title: Heart tube morphogenesis is regulated by segment-specific gene regulatory networks controlled by MEF2C
    Article Snippet: At this stage, the manufacturer’s protocol for Nuclei Isolation for Single Cell Multiome ATAC + Gene Expression Sequencing, Appendix, Low Cell Input Nuclei Isolation (10x Genomics, CG000365 Rev B) was followed exactly to prepare nuclei for library generation. .. Libraries for snRNA-seq and snATAC-seq were prepared according to the manufacturer’s protocol for Chromium Next GEM Single Cell Multiome ATAC + Gene Expression (10x Genomics, CG000338 Rev B), using the 10x Genomics Chromium controller, Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Bundle (10x Genomics, PN-1000283), Chromium Next GEM Chip J Single Cell Kit (10x Genomics, PN-1000234), Single Index Kit N Set A (10x Genomics, PN-1000212), and Dual Index Kit TT Set A (10x Genomics, PN-1000215). ..

    Article Title: Single-cell multiomic analysis reveals the involvement of Type I interferon-responsive CD8+ T cells in amyloid beta-associated memory loss
    Article Snippet: ∼20K cells per sample were used for preparation of the nuclei for the Assay for Transposase-Accessible Chromatin (ATAC) and gene expression libraries using the low cell input nuclei isolation protocol (10x Genomics). .. The Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Bundle (10x Genomics, #1000283), Chromium Next GEM Chip J Single Cell (10x Genomics, #1000234), Dual Index Kit TT Set A (10x Genomics, #1000215), Single Index Kit N Set A (10x Genomics, #1000212) and Chromium Controller were used according to the manufacturer’s protocols. .. For the ATAC library, a sequencing depth of 25K read pairs per nucleus was used with 50bp paired-end reads using NovaSeq or NextSeq (Illumina).

    Sequencing:

    Article Title: Single-nucleus multi-omics of Parkinson's disease reveals a glutamatergic neuronal subtype susceptible to gene dysregulation via alteration of transcriptional networks.
    Article Snippet: In parallel, from the same pool of nuclei from each sample, snRNA-seq libraries were constructed using the Chromium Next GEM Single Cell 3’ GEM, Library, and Gel Bead v3.1 kit, Chip G Single Cell kit, and i7 Multiplex kit (10X Genomics) according to manufacturer’s instructions. .. Parallel snATAC‐seq/snRNA‐seq library preparation and sequencing snATAC-seq libraries were constructed as previously [57] using the Chromium Next GEM Single Cell ATAC Library and Gel Bead v1.1 kit, Chip H Single Cell kit, and Single Index Kit N Set A (10X Genomics) according to manufacturer’s instructions. .. Library quality control was performed on a Bioanalyzer (Agilent) with the High Sensitivity DNA Kit (Agilent) according to manufacturer’s instructions and the 10X Genomics protocols.

    Construct:

    Article Title: Single-nucleus multi-omics of Parkinson's disease reveals a glutamatergic neuronal subtype susceptible to gene dysregulation via alteration of transcriptional networks.
    Article Snippet: In parallel, from the same pool of nuclei from each sample, snRNA-seq libraries were constructed using the Chromium Next GEM Single Cell 3’ GEM, Library, and Gel Bead v3.1 kit, Chip G Single Cell kit, and i7 Multiplex kit (10X Genomics) according to manufacturer’s instructions. .. Parallel snATAC‐seq/snRNA‐seq library preparation and sequencing snATAC-seq libraries were constructed as previously [57] using the Chromium Next GEM Single Cell ATAC Library and Gel Bead v1.1 kit, Chip H Single Cell kit, and Single Index Kit N Set A (10X Genomics) according to manufacturer’s instructions. .. Library quality control was performed on a Bioanalyzer (Agilent) with the High Sensitivity DNA Kit (Agilent) according to manufacturer’s instructions and the 10X Genomics protocols.

    Polymerase Chain Reaction:

    Article Title: Integrative Single-Cell Analysis Reveals Transcriptional and Epigenetic Regulatory Features of Clear Cell Renal Cell Carcinoma
    Article Snippet: Subsequently, GEMs were incubated and cleaned by using Dynabeads (10x Genomics, 2000048) and SPRIselect (Beckman Coulter, B23318). scATAC-seq library construction eliminates the process of reverse transcription compared with scRNA-seq. .. PCR was performed after “Sample Index PCR Mix” and Single Index Kit N Set A (10x Genomics, 1000212) were added into the samples. ..

    Amplification:


    Article Title: Distinct CD8 + T cell dynamics associate with response to neoadjuvant cancer immunotherapies.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER 10x Chromium Next GEM Chip K Single Cell Kit 10X Genomics Cat# 1000286 10x Chromium Next GEM Chip G Single Cell Kit 10X Genomics Cat# 1000120 10x Single Index Kit N Set A 10X Genomics Cat# 1000212 10x Single Index Kit T Set A 10X Genomics Cat# 1000213 10x Dual Index Kit TT Set A 10X Genomics Cat# 1000215 10x Dual Index Kit TN Set A 10X Genomics Cat# 1000250 10x Chromium Single Cell Human TCR Amplification Kit 10X Genomics Cat# 1000252 10x Chromium Single Cell V(D)J Enrichment Kit, Human T Cell 10X Genomics Cat# 1000005 10x Chromium Single Cell 5’ Feature Barcode Library Kit 10X Genomics Cat# 1000080 10x 5’ Feature Barcode Kit, 16 rxns 10X Genomics Cat# 1000256 10X Chromium i7 Multiplex Kit 10X Genomics Cat#120262 DAPI (4’,6-Diamidino-2-Phenylindole, Dihydrochloride) ThermoFisher Scientific Cat# D1306 Opal 6-Plex Detection Kit - for Whole Slide Imaging Akoya Biosciences Cat# NEL871001KT Deposited data Single cell RNA-seq, Single cell TCR-seq and CITE-seq data This study GEO: GSE288199 Single cell RNA-seq and Single cell TCR-seq data van der Leu et al.19 GEO: GSE232240 Single cell RNA-seq and Single cell TCR-seq data Luoma et al.14 GEO: GSE200996 Software and algorithms Cellranger mkfastq v3.0.0 10X Genomics http://software.10xgenomics.com Cellranger v4.0.0 10X Genomics http://software.10xgenomics.com R (v4.0.0 and v4.2.0) The R foundation https://www.r-project.org/ ggpurb (v0.4.0, R package) H. Wickham. ggplot2 https://github.com/kassambara/ggpubr DoubletFinder (v2.0.2) McGinnis et al.70 https://github.com/chris-mcginnis-ucsf/DoubletFinder Seurat (v4.2.0, R package) Hao et al.22 https://satijalab.org/seurat/articles/get_started.html SingleR (v1.2.4, R package) Aran et al.71 Bioconductor msigdbr Dolgaev https://cran.r-project.org/package=msigdbr fgsea (v1.33.2, R package) Korotkevich et al.72 https://github.com/ctlab/fgsea?tab=readme-ov-file Singleseqgset (v0.1.2, R package) Anthony Cillo, Vignali Lab https://github.com/arc85/singleseqgset Vegan Jari Oksanen https://github.com/vegandevs/vegan ComplexHeatmap (v2.4.3, R package) Gu et al.73 https://github.com/jokergoo/ComplexHeatmap STARTRAC (v0.1.0,R package) Zhang et al.55 https://github.com/Japrin/STARTRAC scRepertoire(v1.7.2, R package) Borcherding et al.74 https://github.com/ncborcherding/scRepertoire Slingshot (v0.2.0, R package Street et al.56 https://github.com/kstreet13/slingshot scVelo (v0.2.4, python) Bergen et al.57 https://scvelo.readthedocs.io/en/stable/about.html Velocyto (0.17.16, python) Manno et al.75 https://github.com/velocyto-team/velocyto.py .. REAGENT or RESOURCE SOURCE IDENTIFIER 10x Chromium Next GEM Chip K Single Cell Kit 10X Genomics Cat# 1000286 10x Chromium Next GEM Chip G Single Cell Kit 10X Genomics Cat# 1000120 10x Single Index Kit N Set A 10X Genomics Cat# 1000212 10x Single Index Kit T Set A 10X Genomics Cat# 1000213 10x Dual Index Kit TT Set A 10X Genomics Cat# 1000215 10x Dual Index Kit TN Set A 10X Genomics Cat# 1000250 10x Chromium Single Cell Human TCR Amplification Kit 10X Genomics Cat# 1000252 10x Chromium Single Cell V(D)J Enrichment Kit, Human T Cell 10X Genomics Cat# 1000005 10x Chromium Single Cell 5’ Feature Barcode Library Kit 10X Genomics Cat# 1000080 10x 5’ Feature Barcode Kit, 16 rxns 10X Genomics Cat# 1000256 10X Chromium i7 Multiplex Kit 10X Genomics Cat#120262 DAPI (4’,6-Diamidino-2-Phenylindole, Dihydrochloride) ThermoFisher Scientific Cat# D1306 Opal 6-Plex Detection Kit - for Whole Slide Imaging Akoya Biosciences Cat# NEL871001KT Deposited data Single cell RNA-seq, Single cell TCR-seq and CITE-seq data This study GEO: GSE288199 Single cell RNA-seq and Single cell TCR-seq data van der Leu et al.19 GEO: GSE232240 Single cell RNA-seq and Single cell TCR-seq data Luoma et al.14 GEO: GSE200996 Software and algorithms Cellranger mkfastq v3.0.0 10X Genomics http://software.10xgenomics.com Cellranger v4.0.0 10X Genomics http://software.10xgenomics.com R (v4.0.0 and v4.2.0) The R foundation https://www.r-project.org/ ggpurb (v0.4.0, R package) H. Wickham. ggplot2 https://github.com/kassambara/ggpubr DoubletFinder (v2.0.2) McGinnis et al.70 https://github.com/chris-mcginnis-ucsf/DoubletFinder Seurat (v4.2.0, R package) Hao et al.22 https://satijalab.org/seurat/articles/get_started.html SingleR (v1.2.4, R package) Aran et al.71 Bioconductor msigdbr Dolgaev https://cran.r-project.org/package=msigdbr fgsea (v1.33.2, R package) Korotkevich et al.72 https://github.com/ctlab/fgsea?tab=readme-ov-file Singleseqgset (v0.1.2, R package) Anthony Cillo, Vignali Lab https://github.com/arc85/singleseqgset Vegan Jari Oksanen https://github.com/vegandevs/vegan ComplexHeatmap (v2.4.3, R package) Gu et al.73 https://github.com/jokergoo/ComplexHeatmap STARTRAC (v0.1.0,R package) Zhang et al.55 https://github.com/Japrin/STARTRAC scRepertoire(v1.7.2, R package) Borcherding et al.74 https://github.com/ncborcherding/scRepertoire Slingshot (v0.2.0, R package Street et al.56 https://github.com/kstreet13/slingshot scVelo (v0.2.4, python) Bergen et al.57 https://scvelo.readthedocs.io/en/stable/about.html Velocyto (0.17.16, python) Manno et al.75 https://github.com/velocyto-team/velocyto.py ..

    Article Title: A type 1 immunity-restricted promoter of the IL−33 receptor gene directs antiviral T-cell responses
    Article Snippet: For the preparation of scRNA gene expression (GEX), TCR and CiteSeq libraries, the Chromium Next GEM Single Cell 5’ Library & Gel Bead Kit v1.1 as well as the Chromium Single Cell 5’ Feature Barcode Library Kit were used in conjunction with Chromium Controller (10x Genomics). .. After cDNA amplification the CiteSeq libraries were prepared separately using the Single Index Kit N Set A (10x Genomics). .. TCR target enrichment was performed using the Chromium Single Cell V(D)J Enrichment Kit for mouse T cells (10x Genomics).

    RNA Sequencing:


    Article Title: Distinct CD8 + T cell dynamics associate with response to neoadjuvant cancer immunotherapies.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER 10x Chromium Next GEM Chip K Single Cell Kit 10X Genomics Cat# 1000286 10x Chromium Next GEM Chip G Single Cell Kit 10X Genomics Cat# 1000120 10x Single Index Kit N Set A 10X Genomics Cat# 1000212 10x Single Index Kit T Set A 10X Genomics Cat# 1000213 10x Dual Index Kit TT Set A 10X Genomics Cat# 1000215 10x Dual Index Kit TN Set A 10X Genomics Cat# 1000250 10x Chromium Single Cell Human TCR Amplification Kit 10X Genomics Cat# 1000252 10x Chromium Single Cell V(D)J Enrichment Kit, Human T Cell 10X Genomics Cat# 1000005 10x Chromium Single Cell 5’ Feature Barcode Library Kit 10X Genomics Cat# 1000080 10x 5’ Feature Barcode Kit, 16 rxns 10X Genomics Cat# 1000256 10X Chromium i7 Multiplex Kit 10X Genomics Cat#120262 DAPI (4’,6-Diamidino-2-Phenylindole, Dihydrochloride) ThermoFisher Scientific Cat# D1306 Opal 6-Plex Detection Kit - for Whole Slide Imaging Akoya Biosciences Cat# NEL871001KT Deposited data Single cell RNA-seq, Single cell TCR-seq and CITE-seq data This study GEO: GSE288199 Single cell RNA-seq and Single cell TCR-seq data van der Leu et al.19 GEO: GSE232240 Single cell RNA-seq and Single cell TCR-seq data Luoma et al.14 GEO: GSE200996 Software and algorithms Cellranger mkfastq v3.0.0 10X Genomics http://software.10xgenomics.com Cellranger v4.0.0 10X Genomics http://software.10xgenomics.com R (v4.0.0 and v4.2.0) The R foundation https://www.r-project.org/ ggpurb (v0.4.0, R package) H. Wickham. ggplot2 https://github.com/kassambara/ggpubr DoubletFinder (v2.0.2) McGinnis et al.70 https://github.com/chris-mcginnis-ucsf/DoubletFinder Seurat (v4.2.0, R package) Hao et al.22 https://satijalab.org/seurat/articles/get_started.html SingleR (v1.2.4, R package) Aran et al.71 Bioconductor msigdbr Dolgaev https://cran.r-project.org/package=msigdbr fgsea (v1.33.2, R package) Korotkevich et al.72 https://github.com/ctlab/fgsea?tab=readme-ov-file Singleseqgset (v0.1.2, R package) Anthony Cillo, Vignali Lab https://github.com/arc85/singleseqgset Vegan Jari Oksanen https://github.com/vegandevs/vegan ComplexHeatmap (v2.4.3, R package) Gu et al.73 https://github.com/jokergoo/ComplexHeatmap STARTRAC (v0.1.0,R package) Zhang et al.55 https://github.com/Japrin/STARTRAC scRepertoire(v1.7.2, R package) Borcherding et al.74 https://github.com/ncborcherding/scRepertoire Slingshot (v0.2.0, R package Street et al.56 https://github.com/kstreet13/slingshot scVelo (v0.2.4, python) Bergen et al.57 https://scvelo.readthedocs.io/en/stable/about.html Velocyto (0.17.16, python) Manno et al.75 https://github.com/velocyto-team/velocyto.py .. REAGENT or RESOURCE SOURCE IDENTIFIER 10x Chromium Next GEM Chip K Single Cell Kit 10X Genomics Cat# 1000286 10x Chromium Next GEM Chip G Single Cell Kit 10X Genomics Cat# 1000120 10x Single Index Kit N Set A 10X Genomics Cat# 1000212 10x Single Index Kit T Set A 10X Genomics Cat# 1000213 10x Dual Index Kit TT Set A 10X Genomics Cat# 1000215 10x Dual Index Kit TN Set A 10X Genomics Cat# 1000250 10x Chromium Single Cell Human TCR Amplification Kit 10X Genomics Cat# 1000252 10x Chromium Single Cell V(D)J Enrichment Kit, Human T Cell 10X Genomics Cat# 1000005 10x Chromium Single Cell 5’ Feature Barcode Library Kit 10X Genomics Cat# 1000080 10x 5’ Feature Barcode Kit, 16 rxns 10X Genomics Cat# 1000256 10X Chromium i7 Multiplex Kit 10X Genomics Cat#120262 DAPI (4’,6-Diamidino-2-Phenylindole, Dihydrochloride) ThermoFisher Scientific Cat# D1306 Opal 6-Plex Detection Kit - for Whole Slide Imaging Akoya Biosciences Cat# NEL871001KT Deposited data Single cell RNA-seq, Single cell TCR-seq and CITE-seq data This study GEO: GSE288199 Single cell RNA-seq and Single cell TCR-seq data van der Leu et al.19 GEO: GSE232240 Single cell RNA-seq and Single cell TCR-seq data Luoma et al.14 GEO: GSE200996 Software and algorithms Cellranger mkfastq v3.0.0 10X Genomics http://software.10xgenomics.com Cellranger v4.0.0 10X Genomics http://software.10xgenomics.com R (v4.0.0 and v4.2.0) The R foundation https://www.r-project.org/ ggpurb (v0.4.0, R package) H. Wickham. ggplot2 https://github.com/kassambara/ggpubr DoubletFinder (v2.0.2) McGinnis et al.70 https://github.com/chris-mcginnis-ucsf/DoubletFinder Seurat (v4.2.0, R package) Hao et al.22 https://satijalab.org/seurat/articles/get_started.html SingleR (v1.2.4, R package) Aran et al.71 Bioconductor msigdbr Dolgaev https://cran.r-project.org/package=msigdbr fgsea (v1.33.2, R package) Korotkevich et al.72 https://github.com/ctlab/fgsea?tab=readme-ov-file Singleseqgset (v0.1.2, R package) Anthony Cillo, Vignali Lab https://github.com/arc85/singleseqgset Vegan Jari Oksanen https://github.com/vegandevs/vegan ComplexHeatmap (v2.4.3, R package) Gu et al.73 https://github.com/jokergoo/ComplexHeatmap STARTRAC (v0.1.0,R package) Zhang et al.55 https://github.com/Japrin/STARTRAC scRepertoire(v1.7.2, R package) Borcherding et al.74 https://github.com/ncborcherding/scRepertoire Slingshot (v0.2.0, R package Street et al.56 https://github.com/kstreet13/slingshot scVelo (v0.2.4, python) Bergen et al.57 https://scvelo.readthedocs.io/en/stable/about.html Velocyto (0.17.16, python) Manno et al.75 https://github.com/velocyto-team/velocyto.py ..

    Software:


    Article Title: Distinct CD8 + T cell dynamics associate with response to neoadjuvant cancer immunotherapies.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER 10x Chromium Next GEM Chip K Single Cell Kit 10X Genomics Cat# 1000286 10x Chromium Next GEM Chip G Single Cell Kit 10X Genomics Cat# 1000120 10x Single Index Kit N Set A 10X Genomics Cat# 1000212 10x Single Index Kit T Set A 10X Genomics Cat# 1000213 10x Dual Index Kit TT Set A 10X Genomics Cat# 1000215 10x Dual Index Kit TN Set A 10X Genomics Cat# 1000250 10x Chromium Single Cell Human TCR Amplification Kit 10X Genomics Cat# 1000252 10x Chromium Single Cell V(D)J Enrichment Kit, Human T Cell 10X Genomics Cat# 1000005 10x Chromium Single Cell 5’ Feature Barcode Library Kit 10X Genomics Cat# 1000080 10x 5’ Feature Barcode Kit, 16 rxns 10X Genomics Cat# 1000256 10X Chromium i7 Multiplex Kit 10X Genomics Cat#120262 DAPI (4’,6-Diamidino-2-Phenylindole, Dihydrochloride) ThermoFisher Scientific Cat# D1306 Opal 6-Plex Detection Kit - for Whole Slide Imaging Akoya Biosciences Cat# NEL871001KT Deposited data Single cell RNA-seq, Single cell TCR-seq and CITE-seq data This study GEO: GSE288199 Single cell RNA-seq and Single cell TCR-seq data van der Leu et al.19 GEO: GSE232240 Single cell RNA-seq and Single cell TCR-seq data Luoma et al.14 GEO: GSE200996 Software and algorithms Cellranger mkfastq v3.0.0 10X Genomics http://software.10xgenomics.com Cellranger v4.0.0 10X Genomics http://software.10xgenomics.com R (v4.0.0 and v4.2.0) The R foundation https://www.r-project.org/ ggpurb (v0.4.0, R package) H. Wickham. ggplot2 https://github.com/kassambara/ggpubr DoubletFinder (v2.0.2) McGinnis et al.70 https://github.com/chris-mcginnis-ucsf/DoubletFinder Seurat (v4.2.0, R package) Hao et al.22 https://satijalab.org/seurat/articles/get_started.html SingleR (v1.2.4, R package) Aran et al.71 Bioconductor msigdbr Dolgaev https://cran.r-project.org/package=msigdbr fgsea (v1.33.2, R package) Korotkevich et al.72 https://github.com/ctlab/fgsea?tab=readme-ov-file Singleseqgset (v0.1.2, R package) Anthony Cillo, Vignali Lab https://github.com/arc85/singleseqgset Vegan Jari Oksanen https://github.com/vegandevs/vegan ComplexHeatmap (v2.4.3, R package) Gu et al.73 https://github.com/jokergoo/ComplexHeatmap STARTRAC (v0.1.0,R package) Zhang et al.55 https://github.com/Japrin/STARTRAC scRepertoire(v1.7.2, R package) Borcherding et al.74 https://github.com/ncborcherding/scRepertoire Slingshot (v0.2.0, R package Street et al.56 https://github.com/kstreet13/slingshot scVelo (v0.2.4, python) Bergen et al.57 https://scvelo.readthedocs.io/en/stable/about.html Velocyto (0.17.16, python) Manno et al.75 https://github.com/velocyto-team/velocyto.py .. REAGENT or RESOURCE SOURCE IDENTIFIER 10x Chromium Next GEM Chip K Single Cell Kit 10X Genomics Cat# 1000286 10x Chromium Next GEM Chip G Single Cell Kit 10X Genomics Cat# 1000120 10x Single Index Kit N Set A 10X Genomics Cat# 1000212 10x Single Index Kit T Set A 10X Genomics Cat# 1000213 10x Dual Index Kit TT Set A 10X Genomics Cat# 1000215 10x Dual Index Kit TN Set A 10X Genomics Cat# 1000250 10x Chromium Single Cell Human TCR Amplification Kit 10X Genomics Cat# 1000252 10x Chromium Single Cell V(D)J Enrichment Kit, Human T Cell 10X Genomics Cat# 1000005 10x Chromium Single Cell 5’ Feature Barcode Library Kit 10X Genomics Cat# 1000080 10x 5’ Feature Barcode Kit, 16 rxns 10X Genomics Cat# 1000256 10X Chromium i7 Multiplex Kit 10X Genomics Cat#120262 DAPI (4’,6-Diamidino-2-Phenylindole, Dihydrochloride) ThermoFisher Scientific Cat# D1306 Opal 6-Plex Detection Kit - for Whole Slide Imaging Akoya Biosciences Cat# NEL871001KT Deposited data Single cell RNA-seq, Single cell TCR-seq and CITE-seq data This study GEO: GSE288199 Single cell RNA-seq and Single cell TCR-seq data van der Leu et al.19 GEO: GSE232240 Single cell RNA-seq and Single cell TCR-seq data Luoma et al.14 GEO: GSE200996 Software and algorithms Cellranger mkfastq v3.0.0 10X Genomics http://software.10xgenomics.com Cellranger v4.0.0 10X Genomics http://software.10xgenomics.com R (v4.0.0 and v4.2.0) The R foundation https://www.r-project.org/ ggpurb (v0.4.0, R package) H. Wickham. ggplot2 https://github.com/kassambara/ggpubr DoubletFinder (v2.0.2) McGinnis et al.70 https://github.com/chris-mcginnis-ucsf/DoubletFinder Seurat (v4.2.0, R package) Hao et al.22 https://satijalab.org/seurat/articles/get_started.html SingleR (v1.2.4, R package) Aran et al.71 Bioconductor msigdbr Dolgaev https://cran.r-project.org/package=msigdbr fgsea (v1.33.2, R package) Korotkevich et al.72 https://github.com/ctlab/fgsea?tab=readme-ov-file Singleseqgset (v0.1.2, R package) Anthony Cillo, Vignali Lab https://github.com/arc85/singleseqgset Vegan Jari Oksanen https://github.com/vegandevs/vegan ComplexHeatmap (v2.4.3, R package) Gu et al.73 https://github.com/jokergoo/ComplexHeatmap STARTRAC (v0.1.0,R package) Zhang et al.55 https://github.com/Japrin/STARTRAC scRepertoire(v1.7.2, R package) Borcherding et al.74 https://github.com/ncborcherding/scRepertoire Slingshot (v0.2.0, R package Street et al.56 https://github.com/kstreet13/slingshot scVelo (v0.2.4, python) Bergen et al.57 https://scvelo.readthedocs.io/en/stable/about.html Velocyto (0.17.16, python) Manno et al.75 https://github.com/velocyto-team/velocyto.py ..

    Expressing:


    Multiplex Assay:

    Article Title: Distinct CD8 + T cell dynamics associate with response to neoadjuvant cancer immunotherapies.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER 10x Chromium Next GEM Chip K Single Cell Kit 10X Genomics Cat# 1000286 10x Chromium Next GEM Chip G Single Cell Kit 10X Genomics Cat# 1000120 10x Single Index Kit N Set A 10X Genomics Cat# 1000212 10x Single Index Kit T Set A 10X Genomics Cat# 1000213 10x Dual Index Kit TT Set A 10X Genomics Cat# 1000215 10x Dual Index Kit TN Set A 10X Genomics Cat# 1000250 10x Chromium Single Cell Human TCR Amplification Kit 10X Genomics Cat# 1000252 10x Chromium Single Cell V(D)J Enrichment Kit, Human T Cell 10X Genomics Cat# 1000005 10x Chromium Single Cell 5’ Feature Barcode Library Kit 10X Genomics Cat# 1000080 10x 5’ Feature Barcode Kit, 16 rxns 10X Genomics Cat# 1000256 10X Chromium i7 Multiplex Kit 10X Genomics Cat#120262 DAPI (4’,6-Diamidino-2-Phenylindole, Dihydrochloride) ThermoFisher Scientific Cat# D1306 Opal 6-Plex Detection Kit - for Whole Slide Imaging Akoya Biosciences Cat# NEL871001KT Deposited data Single cell RNA-seq, Single cell TCR-seq and CITE-seq data This study GEO: GSE288199 Single cell RNA-seq and Single cell TCR-seq data van der Leu et al.19 GEO: GSE232240 Single cell RNA-seq and Single cell TCR-seq data Luoma et al.14 GEO: GSE200996 Software and algorithms Cellranger mkfastq v3.0.0 10X Genomics http://software.10xgenomics.com Cellranger v4.0.0 10X Genomics http://software.10xgenomics.com R (v4.0.0 and v4.2.0) The R foundation https://www.r-project.org/ ggpurb (v0.4.0, R package) H. Wickham. ggplot2 https://github.com/kassambara/ggpubr DoubletFinder (v2.0.2) McGinnis et al.70 https://github.com/chris-mcginnis-ucsf/DoubletFinder Seurat (v4.2.0, R package) Hao et al.22 https://satijalab.org/seurat/articles/get_started.html SingleR (v1.2.4, R package) Aran et al.71 Bioconductor msigdbr Dolgaev https://cran.r-project.org/package=msigdbr fgsea (v1.33.2, R package) Korotkevich et al.72 https://github.com/ctlab/fgsea?tab=readme-ov-file Singleseqgset (v0.1.2, R package) Anthony Cillo, Vignali Lab https://github.com/arc85/singleseqgset Vegan Jari Oksanen https://github.com/vegandevs/vegan ComplexHeatmap (v2.4.3, R package) Gu et al.73 https://github.com/jokergoo/ComplexHeatmap STARTRAC (v0.1.0,R package) Zhang et al.55 https://github.com/Japrin/STARTRAC scRepertoire(v1.7.2, R package) Borcherding et al.74 https://github.com/ncborcherding/scRepertoire Slingshot (v0.2.0, R package Street et al.56 https://github.com/kstreet13/slingshot scVelo (v0.2.4, python) Bergen et al.57 https://scvelo.readthedocs.io/en/stable/about.html Velocyto (0.17.16, python) Manno et al.75 https://github.com/velocyto-team/velocyto.py .. REAGENT or RESOURCE SOURCE IDENTIFIER 10x Chromium Next GEM Chip K Single Cell Kit 10X Genomics Cat# 1000286 10x Chromium Next GEM Chip G Single Cell Kit 10X Genomics Cat# 1000120 10x Single Index Kit N Set A 10X Genomics Cat# 1000212 10x Single Index Kit T Set A 10X Genomics Cat# 1000213 10x Dual Index Kit TT Set A 10X Genomics Cat# 1000215 10x Dual Index Kit TN Set A 10X Genomics Cat# 1000250 10x Chromium Single Cell Human TCR Amplification Kit 10X Genomics Cat# 1000252 10x Chromium Single Cell V(D)J Enrichment Kit, Human T Cell 10X Genomics Cat# 1000005 10x Chromium Single Cell 5’ Feature Barcode Library Kit 10X Genomics Cat# 1000080 10x 5’ Feature Barcode Kit, 16 rxns 10X Genomics Cat# 1000256 10X Chromium i7 Multiplex Kit 10X Genomics Cat#120262 DAPI (4’,6-Diamidino-2-Phenylindole, Dihydrochloride) ThermoFisher Scientific Cat# D1306 Opal 6-Plex Detection Kit - for Whole Slide Imaging Akoya Biosciences Cat# NEL871001KT Deposited data Single cell RNA-seq, Single cell TCR-seq and CITE-seq data This study GEO: GSE288199 Single cell RNA-seq and Single cell TCR-seq data van der Leu et al.19 GEO: GSE232240 Single cell RNA-seq and Single cell TCR-seq data Luoma et al.14 GEO: GSE200996 Software and algorithms Cellranger mkfastq v3.0.0 10X Genomics http://software.10xgenomics.com Cellranger v4.0.0 10X Genomics http://software.10xgenomics.com R (v4.0.0 and v4.2.0) The R foundation https://www.r-project.org/ ggpurb (v0.4.0, R package) H. Wickham. ggplot2 https://github.com/kassambara/ggpubr DoubletFinder (v2.0.2) McGinnis et al.70 https://github.com/chris-mcginnis-ucsf/DoubletFinder Seurat (v4.2.0, R package) Hao et al.22 https://satijalab.org/seurat/articles/get_started.html SingleR (v1.2.4, R package) Aran et al.71 Bioconductor msigdbr Dolgaev https://cran.r-project.org/package=msigdbr fgsea (v1.33.2, R package) Korotkevich et al.72 https://github.com/ctlab/fgsea?tab=readme-ov-file Singleseqgset (v0.1.2, R package) Anthony Cillo, Vignali Lab https://github.com/arc85/singleseqgset Vegan Jari Oksanen https://github.com/vegandevs/vegan ComplexHeatmap (v2.4.3, R package) Gu et al.73 https://github.com/jokergoo/ComplexHeatmap STARTRAC (v0.1.0,R package) Zhang et al.55 https://github.com/Japrin/STARTRAC scRepertoire(v1.7.2, R package) Borcherding et al.74 https://github.com/ncborcherding/scRepertoire Slingshot (v0.2.0, R package Street et al.56 https://github.com/kstreet13/slingshot scVelo (v0.2.4, python) Bergen et al.57 https://scvelo.readthedocs.io/en/stable/about.html Velocyto (0.17.16, python) Manno et al.75 https://github.com/velocyto-team/velocyto.py ..

    Imaging:

    Article Title: Distinct CD8 + T cell dynamics associate with response to neoadjuvant cancer immunotherapies.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER 10x Chromium Next GEM Chip K Single Cell Kit 10X Genomics Cat# 1000286 10x Chromium Next GEM Chip G Single Cell Kit 10X Genomics Cat# 1000120 10x Single Index Kit N Set A 10X Genomics Cat# 1000212 10x Single Index Kit T Set A 10X Genomics Cat# 1000213 10x Dual Index Kit TT Set A 10X Genomics Cat# 1000215 10x Dual Index Kit TN Set A 10X Genomics Cat# 1000250 10x Chromium Single Cell Human TCR Amplification Kit 10X Genomics Cat# 1000252 10x Chromium Single Cell V(D)J Enrichment Kit, Human T Cell 10X Genomics Cat# 1000005 10x Chromium Single Cell 5’ Feature Barcode Library Kit 10X Genomics Cat# 1000080 10x 5’ Feature Barcode Kit, 16 rxns 10X Genomics Cat# 1000256 10X Chromium i7 Multiplex Kit 10X Genomics Cat#120262 DAPI (4’,6-Diamidino-2-Phenylindole, Dihydrochloride) ThermoFisher Scientific Cat# D1306 Opal 6-Plex Detection Kit - for Whole Slide Imaging Akoya Biosciences Cat# NEL871001KT Deposited data Single cell RNA-seq, Single cell TCR-seq and CITE-seq data This study GEO: GSE288199 Single cell RNA-seq and Single cell TCR-seq data van der Leu et al.19 GEO: GSE232240 Single cell RNA-seq and Single cell TCR-seq data Luoma et al.14 GEO: GSE200996 Software and algorithms Cellranger mkfastq v3.0.0 10X Genomics http://software.10xgenomics.com Cellranger v4.0.0 10X Genomics http://software.10xgenomics.com R (v4.0.0 and v4.2.0) The R foundation https://www.r-project.org/ ggpurb (v0.4.0, R package) H. Wickham. ggplot2 https://github.com/kassambara/ggpubr DoubletFinder (v2.0.2) McGinnis et al.70 https://github.com/chris-mcginnis-ucsf/DoubletFinder Seurat (v4.2.0, R package) Hao et al.22 https://satijalab.org/seurat/articles/get_started.html SingleR (v1.2.4, R package) Aran et al.71 Bioconductor msigdbr Dolgaev https://cran.r-project.org/package=msigdbr fgsea (v1.33.2, R package) Korotkevich et al.72 https://github.com/ctlab/fgsea?tab=readme-ov-file Singleseqgset (v0.1.2, R package) Anthony Cillo, Vignali Lab https://github.com/arc85/singleseqgset Vegan Jari Oksanen https://github.com/vegandevs/vegan ComplexHeatmap (v2.4.3, R package) Gu et al.73 https://github.com/jokergoo/ComplexHeatmap STARTRAC (v0.1.0,R package) Zhang et al.55 https://github.com/Japrin/STARTRAC scRepertoire(v1.7.2, R package) Borcherding et al.74 https://github.com/ncborcherding/scRepertoire Slingshot (v0.2.0, R package Street et al.56 https://github.com/kstreet13/slingshot scVelo (v0.2.4, python) Bergen et al.57 https://scvelo.readthedocs.io/en/stable/about.html Velocyto (0.17.16, python) Manno et al.75 https://github.com/velocyto-team/velocyto.py .. REAGENT or RESOURCE SOURCE IDENTIFIER 10x Chromium Next GEM Chip K Single Cell Kit 10X Genomics Cat# 1000286 10x Chromium Next GEM Chip G Single Cell Kit 10X Genomics Cat# 1000120 10x Single Index Kit N Set A 10X Genomics Cat# 1000212 10x Single Index Kit T Set A 10X Genomics Cat# 1000213 10x Dual Index Kit TT Set A 10X Genomics Cat# 1000215 10x Dual Index Kit TN Set A 10X Genomics Cat# 1000250 10x Chromium Single Cell Human TCR Amplification Kit 10X Genomics Cat# 1000252 10x Chromium Single Cell V(D)J Enrichment Kit, Human T Cell 10X Genomics Cat# 1000005 10x Chromium Single Cell 5’ Feature Barcode Library Kit 10X Genomics Cat# 1000080 10x 5’ Feature Barcode Kit, 16 rxns 10X Genomics Cat# 1000256 10X Chromium i7 Multiplex Kit 10X Genomics Cat#120262 DAPI (4’,6-Diamidino-2-Phenylindole, Dihydrochloride) ThermoFisher Scientific Cat# D1306 Opal 6-Plex Detection Kit - for Whole Slide Imaging Akoya Biosciences Cat# NEL871001KT Deposited data Single cell RNA-seq, Single cell TCR-seq and CITE-seq data This study GEO: GSE288199 Single cell RNA-seq and Single cell TCR-seq data van der Leu et al.19 GEO: GSE232240 Single cell RNA-seq and Single cell TCR-seq data Luoma et al.14 GEO: GSE200996 Software and algorithms Cellranger mkfastq v3.0.0 10X Genomics http://software.10xgenomics.com Cellranger v4.0.0 10X Genomics http://software.10xgenomics.com R (v4.0.0 and v4.2.0) The R foundation https://www.r-project.org/ ggpurb (v0.4.0, R package) H. Wickham. ggplot2 https://github.com/kassambara/ggpubr DoubletFinder (v2.0.2) McGinnis et al.70 https://github.com/chris-mcginnis-ucsf/DoubletFinder Seurat (v4.2.0, R package) Hao et al.22 https://satijalab.org/seurat/articles/get_started.html SingleR (v1.2.4, R package) Aran et al.71 Bioconductor msigdbr Dolgaev https://cran.r-project.org/package=msigdbr fgsea (v1.33.2, R package) Korotkevich et al.72 https://github.com/ctlab/fgsea?tab=readme-ov-file Singleseqgset (v0.1.2, R package) Anthony Cillo, Vignali Lab https://github.com/arc85/singleseqgset Vegan Jari Oksanen https://github.com/vegandevs/vegan ComplexHeatmap (v2.4.3, R package) Gu et al.73 https://github.com/jokergoo/ComplexHeatmap STARTRAC (v0.1.0,R package) Zhang et al.55 https://github.com/Japrin/STARTRAC scRepertoire(v1.7.2, R package) Borcherding et al.74 https://github.com/ncborcherding/scRepertoire Slingshot (v0.2.0, R package Street et al.56 https://github.com/kstreet13/slingshot scVelo (v0.2.4, python) Bergen et al.57 https://scvelo.readthedocs.io/en/stable/about.html Velocyto (0.17.16, python) Manno et al.75 https://github.com/velocyto-team/velocyto.py ..

    Generated:

    Article Title: Human microglia maturation is underpinned by specific gene regulatory networks.
    Article Snippet: .. Up to 15,300 nuclei were tagmented before loading onto a Chromium Controller; libraries were generated according to manufacturer specifications (Chromium Next GEM Single Cell ATAC Library and Gel Bead Kit v1.1, 1000175; Chromium Next GEM Chip H Single Cell Kit, 1000162; Single Index Kit N Set A, 1000212, 10x Genomics). ..



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