Multiplex Assay:
Article Title: Phylogenomics and classification of Cactaceae based on hundreds of nuclear genes
Article Snippet: Briefly, using a modified CTAB protocol (Doyle and Doyle ), we extracted DNA which we then fragmented using sonication (Covaris M220 Focused-ultrasonicator with microTUBEs AFA Fiber Pre-Slit Snap-Cap; Woburn, MA, USA) when DNA fragment length exceeded 350 bp. .. We prepared Dual-indexed libraries for Illumina sequencing using the DNA NEBNext UltraTM II Library Prep Kit at half the recommended volume, with Dual Index Primers Set 1, NEBNext Multiplex Oligos for Illumina (New England BioLabs). .. After pooling 20–25 DNA libraries (equimolar for a total of 1 μg of DNA), we hybridized them using the Angiosperms353 v1 expert panel (Arbor Biosciences, Ann Arbor, MI, USA; Catalog #308,196; Johnson et al. ) at 65 °C for 28–32 h. After amplifying enriched products for 10 cycles and cleaning them, we quantified and multiplexed them and then sequenced them on an Illumina MiSeq (v3 reagents, 2 × 300-bp paired-end reads, Illumina, San Diego, CA, USA) at the Royal Botanic Gardens, Kew, or on an on Illumina HiSeq (2 × 150-bp paired-end reads) at Genewiz (Takeley, UK).
Article Title: Pol θ-mediated end-joining uses microhomologies containing mismatches.
Article Snippet: The reactions were assembled in 3 × 50 μL mixtures (1X NEBNext® UltraTM II Q5® Master Mix (M0544L, New England Biolabs) with 0.5 μM primers (ASP-ForL/ASP-RewL) and 2 μL eluate. .. To attach the Illumina adapter and indexes for each library (Supplementary Data 1), a second round of PCR (100 μL, six cycles) was conducted using 120 ng of the first round PCR purified products plus the Dual Index Primers Set 1 from NEBNext® Multiplex Oligos for Illumina (E7600S, New England Biolabs). .. QIAquick Gel Extraction Kit (28004, QIAGEN) was then used to obtain a 30 μL eluate of the reaction products containing the Illumina adapters.
Article Title: AAVs targeting human carbonic anhydrase IV enhance gene delivery to the brain
Article Snippet: DNA was extracted using the Quick-DNA/RNA viral kit (Zymo, D7021) following the manufacturer’s protocol. .. Dual Index primers (NEB, NEBNext Multiplex Oligos for Illumina) were used to add indexes for next-generation sequencing (NGS). .. Dual Index primers (NEB, NEBNext Multiplex Oligos for Illumina) were used to add indexes for next-generation sequencing (NGS).
Article Title: Spatial regulation of CD8 + T cells at the HLA-E-NKG2A axis drives HIV persistence in lymph node B cell follicles.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER NEBNext ultra-RNA library preparation kit NEB Cat# E7530 (replaced by NEB #E7770). .. Nextera DNA library kit Illumina 15028212 Deposited data Lymph node ATAC-Seq and RNA-seq data GEO: GSE180532 31 N/A PBMC ATAC-Seq and RNA-seq data GEO: GSE297327 N/A Oligonucleotides Nextera Index kit Illumina 15055289 NEBNext multiplex oligos for Illumina, Dual Index Primers set 1 NEB E7600S GeoMx Immune Pathways panel Bruker (Nanostring) 121300201 Software and algorithms StrataQuest v7.1.1.1.143 TissueGnostics RRID:SCR_024861 CellProfiler Carpenter et al. 60 ; Ward et al. 61 RRID:SCR_007358 CytoMap Stoltzfus et al. 62 RRID:SCR_021227 FCS Express v7.18.0025 De Novo Software RRID:SCR_016431 GeoMx DSP software Bruker (Nanostring) N/A GraphPad Prism v9.5.1 www.GraphPad.com RRID:SCR_002798 ATAC-seq and RNA-seq analysis pipeline codes This paper at https://doi.org/10.5281/ zenodo.16575923 (https://github.com/ TheWhyofFry/ndhlovucellreports2025) and subsequent packages N/A TrimGalore Kundaje lab, Sloan et al. 63 N/A clusterProfiler Illumina, Yu et al. 64 RRID:SCR_016884 Diffbind and EdgeR Robinson et al. 65 RRID:SCR_012918; RRID:SCR_012802 ChIPSeeker Yu et al. 66 RRID:SCR_021322 Kallisto Bray et al. 67 RRID:SCR_016582 Ensembl version 85 (GRCh37) Dyer et al. 68 N/A Sleuth R package Pimentel et al. 69 RRID:SCR_016883 limma R package Ritchie et al. 70 RRID:SCR_010943 Correlation matrix codes This paper at https://doi.org/10.5281/ zenodo.16572491 (https://github.com/ AndreaO1125/Gex_corrplot) and https:// statsandr.com/blog/correlationcoefficient-and-correlation-test-in-r/ N/A R version 4.2.2 R: A Language and Environment for Statistical Computing 33 https://www.Rproject.org/ RRID:SCR_001905 Hmisc R package Harrell 35 https://CRAN.R-project.org/ package=Hmisc RRID:SCR_022947 Corrplot R package Wei and Simko 34 https://github.com/taiyun/ corrplot RRID:SCR_024683 FACS Diva BD RRID:SCR_001456 FlowJo 10.0.8 Flowjo LLC RRID:SCR_008520 UMAP plugin v4.1.1 McInnes et al. 71 N/A FlowSOM v2.6.0 Van Gassen et al. 72 RRID:SCR_016899 Flow cytometry UMAP codes This paper at https://doi.org/10.5281/ zenodo.16572922 (https://github.com/ AndreaO1125/T_cell_umaps) and subsequent packages N/A ggPlot2 R package Wickham 73 https://ggplot2.tidyverse.org RRID:SCR_014601 dplyr R package Wickham et al. 74 https://dplyr.tidyverse.org N/A 16 Cell Reports 44, 116181, September 23, 2025 ..
Next-Generation Sequencing:
Article Title: AAVs targeting human carbonic anhydrase IV enhance gene delivery to the brain
Article Snippet: DNA was extracted using the Quick-DNA/RNA viral kit (Zymo, D7021) following the manufacturer’s protocol. .. Dual Index primers (NEB, NEBNext Multiplex Oligos for Illumina) were used to add indexes for next-generation sequencing (NGS). .. Dual Index primers (NEB, NEBNext Multiplex Oligos for Illumina) were used to add indexes for next-generation sequencing (NGS).
Polymerase Chain Reaction:Article Title: Pol θ-mediated end-joining uses microhomologies containing mismatches.
Article Snippet: The reactions were assembled in 3 × 50 μL mixtures (1X NEBNext® UltraTM II Q5® Master Mix (M0544L, New England Biolabs) with 0.5 μM primers (ASP-ForL/ASP-RewL) and 2 μL eluate. .. To attach the Illumina adapter and indexes for each library (Supplementary Data 1), a second round of PCR (100 μL, six cycles) was conducted using 120 ng of the first round PCR purified products plus the Dual Index Primers Set 1 from NEBNext® Multiplex Oligos for Illumina (E7600S, New England Biolabs). .. QIAquick Gel Extraction Kit (28004, QIAGEN) was then used to obtain a 30 μL eluate of the reaction products containing the Illumina adapters.
Purification:Article Title: Pol θ-mediated end-joining uses microhomologies containing mismatches.
Article Snippet: The reactions were assembled in 3 × 50 μL mixtures (1X NEBNext® UltraTM II Q5® Master Mix (M0544L, New England Biolabs) with 0.5 μM primers (ASP-ForL/ASP-RewL) and 2 μL eluate. .. To attach the Illumina adapter and indexes for each library (Supplementary Data 1), a second round of PCR (100 μL, six cycles) was conducted using 120 ng of the first round PCR purified products plus the Dual Index Primers Set 1 from NEBNext® Multiplex Oligos for Illumina (E7600S, New England Biolabs). .. QIAquick Gel Extraction Kit (28004, QIAGEN) was then used to obtain a 30 μL eluate of the reaction products containing the Illumina adapters.
RNA Sequencing:Article Title: Spatial regulation of CD8 + T cells at the HLA-E-NKG2A axis drives HIV persistence in lymph node B cell follicles.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER NEBNext ultra-RNA library preparation kit NEB Cat# E7530 (replaced by NEB #E7770). .. Nextera DNA library kit Illumina 15028212 Deposited data Lymph node ATAC-Seq and RNA-seq data GEO: GSE180532 31 N/A PBMC ATAC-Seq and RNA-seq data GEO: GSE297327 N/A Oligonucleotides Nextera Index kit Illumina 15055289 NEBNext multiplex oligos for Illumina, Dual Index Primers set 1 NEB E7600S GeoMx Immune Pathways panel Bruker (Nanostring) 121300201 Software and algorithms StrataQuest v7.1.1.1.143 TissueGnostics RRID:SCR_024861 CellProfiler Carpenter et al. 60 ; Ward et al. 61 RRID:SCR_007358 CytoMap Stoltzfus et al. 62 RRID:SCR_021227 FCS Express v7.18.0025 De Novo Software RRID:SCR_016431 GeoMx DSP software Bruker (Nanostring) N/A GraphPad Prism v9.5.1 www.GraphPad.com RRID:SCR_002798 ATAC-seq and RNA-seq analysis pipeline codes This paper at https://doi.org/10.5281/ zenodo.16575923 (https://github.com/ TheWhyofFry/ndhlovucellreports2025) and subsequent packages N/A TrimGalore Kundaje lab, Sloan et al. 63 N/A clusterProfiler Illumina, Yu et al. 64 RRID:SCR_016884 Diffbind and EdgeR Robinson et al. 65 RRID:SCR_012918; RRID:SCR_012802 ChIPSeeker Yu et al. 66 RRID:SCR_021322 Kallisto Bray et al. 67 RRID:SCR_016582 Ensembl version 85 (GRCh37) Dyer et al. 68 N/A Sleuth R package Pimentel et al. 69 RRID:SCR_016883 limma R package Ritchie et al. 70 RRID:SCR_010943 Correlation matrix codes This paper at https://doi.org/10.5281/ zenodo.16572491 (https://github.com/ AndreaO1125/Gex_corrplot) and https:// statsandr.com/blog/correlationcoefficient-and-correlation-test-in-r/ N/A R version 4.2.2 R: A Language and Environment for Statistical Computing 33 https://www.Rproject.org/ RRID:SCR_001905 Hmisc R package Harrell 35 https://CRAN.R-project.org/ package=Hmisc RRID:SCR_022947 Corrplot R package Wei and Simko 34 https://github.com/taiyun/ corrplot RRID:SCR_024683 FACS Diva BD RRID:SCR_001456 FlowJo 10.0.8 Flowjo LLC RRID:SCR_008520 UMAP plugin v4.1.1 McInnes et al. 71 N/A FlowSOM v2.6.0 Van Gassen et al. 72 RRID:SCR_016899 Flow cytometry UMAP codes This paper at https://doi.org/10.5281/ zenodo.16572922 (https://github.com/ AndreaO1125/T_cell_umaps) and subsequent packages N/A ggPlot2 R package Wickham 73 https://ggplot2.tidyverse.org RRID:SCR_014601 dplyr R package Wickham et al. 74 https://dplyr.tidyverse.org N/A 16 Cell Reports 44, 116181, September 23, 2025 ..
Software:Article Title: Spatial regulation of CD8 + T cells at the HLA-E-NKG2A axis drives HIV persistence in lymph node B cell follicles.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER NEBNext ultra-RNA library preparation kit NEB Cat# E7530 (replaced by NEB #E7770). .. Nextera DNA library kit Illumina 15028212 Deposited data Lymph node ATAC-Seq and RNA-seq data GEO: GSE180532 31 N/A PBMC ATAC-Seq and RNA-seq data GEO: GSE297327 N/A Oligonucleotides Nextera Index kit Illumina 15055289 NEBNext multiplex oligos for Illumina, Dual Index Primers set 1 NEB E7600S GeoMx Immune Pathways panel Bruker (Nanostring) 121300201 Software and algorithms StrataQuest v7.1.1.1.143 TissueGnostics RRID:SCR_024861 CellProfiler Carpenter et al. 60 ; Ward et al. 61 RRID:SCR_007358 CytoMap Stoltzfus et al. 62 RRID:SCR_021227 FCS Express v7.18.0025 De Novo Software RRID:SCR_016431 GeoMx DSP software Bruker (Nanostring) N/A GraphPad Prism v9.5.1 www.GraphPad.com RRID:SCR_002798 ATAC-seq and RNA-seq analysis pipeline codes This paper at https://doi.org/10.5281/ zenodo.16575923 (https://github.com/ TheWhyofFry/ndhlovucellreports2025) and subsequent packages N/A TrimGalore Kundaje lab, Sloan et al. 63 N/A clusterProfiler Illumina, Yu et al. 64 RRID:SCR_016884 Diffbind and EdgeR Robinson et al. 65 RRID:SCR_012918; RRID:SCR_012802 ChIPSeeker Yu et al. 66 RRID:SCR_021322 Kallisto Bray et al. 67 RRID:SCR_016582 Ensembl version 85 (GRCh37) Dyer et al. 68 N/A Sleuth R package Pimentel et al. 69 RRID:SCR_016883 limma R package Ritchie et al. 70 RRID:SCR_010943 Correlation matrix codes This paper at https://doi.org/10.5281/ zenodo.16572491 (https://github.com/ AndreaO1125/Gex_corrplot) and https:// statsandr.com/blog/correlationcoefficient-and-correlation-test-in-r/ N/A R version 4.2.2 R: A Language and Environment for Statistical Computing 33 https://www.Rproject.org/ RRID:SCR_001905 Hmisc R package Harrell 35 https://CRAN.R-project.org/ package=Hmisc RRID:SCR_022947 Corrplot R package Wei and Simko 34 https://github.com/taiyun/ corrplot RRID:SCR_024683 FACS Diva BD RRID:SCR_001456 FlowJo 10.0.8 Flowjo LLC RRID:SCR_008520 UMAP plugin v4.1.1 McInnes et al. 71 N/A FlowSOM v2.6.0 Van Gassen et al. 72 RRID:SCR_016899 Flow cytometry UMAP codes This paper at https://doi.org/10.5281/ zenodo.16572922 (https://github.com/ AndreaO1125/T_cell_umaps) and subsequent packages N/A ggPlot2 R package Wickham 73 https://ggplot2.tidyverse.org RRID:SCR_014601 dplyr R package Wickham et al. 74 https://dplyr.tidyverse.org N/A 16 Cell Reports 44, 116181, September 23, 2025 ..
FACS:Article Title: Spatial regulation of CD8 + T cells at the HLA-E-NKG2A axis drives HIV persistence in lymph node B cell follicles.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER NEBNext ultra-RNA library preparation kit NEB Cat# E7530 (replaced by NEB #E7770). .. Nextera DNA library kit Illumina 15028212 Deposited data Lymph node ATAC-Seq and RNA-seq data GEO: GSE180532 31 N/A PBMC ATAC-Seq and RNA-seq data GEO: GSE297327 N/A Oligonucleotides Nextera Index kit Illumina 15055289 NEBNext multiplex oligos for Illumina, Dual Index Primers set 1 NEB E7600S GeoMx Immune Pathways panel Bruker (Nanostring) 121300201 Software and algorithms StrataQuest v7.1.1.1.143 TissueGnostics RRID:SCR_024861 CellProfiler Carpenter et al. 60 ; Ward et al. 61 RRID:SCR_007358 CytoMap Stoltzfus et al. 62 RRID:SCR_021227 FCS Express v7.18.0025 De Novo Software RRID:SCR_016431 GeoMx DSP software Bruker (Nanostring) N/A GraphPad Prism v9.5.1 www.GraphPad.com RRID:SCR_002798 ATAC-seq and RNA-seq analysis pipeline codes This paper at https://doi.org/10.5281/ zenodo.16575923 (https://github.com/ TheWhyofFry/ndhlovucellreports2025) and subsequent packages N/A TrimGalore Kundaje lab, Sloan et al. 63 N/A clusterProfiler Illumina, Yu et al. 64 RRID:SCR_016884 Diffbind and EdgeR Robinson et al. 65 RRID:SCR_012918; RRID:SCR_012802 ChIPSeeker Yu et al. 66 RRID:SCR_021322 Kallisto Bray et al. 67 RRID:SCR_016582 Ensembl version 85 (GRCh37) Dyer et al. 68 N/A Sleuth R package Pimentel et al. 69 RRID:SCR_016883 limma R package Ritchie et al. 70 RRID:SCR_010943 Correlation matrix codes This paper at https://doi.org/10.5281/ zenodo.16572491 (https://github.com/ AndreaO1125/Gex_corrplot) and https:// statsandr.com/blog/correlationcoefficient-and-correlation-test-in-r/ N/A R version 4.2.2 R: A Language and Environment for Statistical Computing 33 https://www.Rproject.org/ RRID:SCR_001905 Hmisc R package Harrell 35 https://CRAN.R-project.org/ package=Hmisc RRID:SCR_022947 Corrplot R package Wei and Simko 34 https://github.com/taiyun/ corrplot RRID:SCR_024683 FACS Diva BD RRID:SCR_001456 FlowJo 10.0.8 Flowjo LLC RRID:SCR_008520 UMAP plugin v4.1.1 McInnes et al. 71 N/A FlowSOM v2.6.0 Van Gassen et al. 72 RRID:SCR_016899 Flow cytometry UMAP codes This paper at https://doi.org/10.5281/ zenodo.16572922 (https://github.com/ AndreaO1125/T_cell_umaps) and subsequent packages N/A ggPlot2 R package Wickham 73 https://ggplot2.tidyverse.org RRID:SCR_014601 dplyr R package Wickham et al. 74 https://dplyr.tidyverse.org N/A 16 Cell Reports 44, 116181, September 23, 2025 ..
Flow Cytometry:Article Title: Spatial regulation of CD8 + T cells at the HLA-E-NKG2A axis drives HIV persistence in lymph node B cell follicles.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER NEBNext ultra-RNA library preparation kit NEB Cat# E7530 (replaced by NEB #E7770). .. Nextera DNA library kit Illumina 15028212 Deposited data Lymph node ATAC-Seq and RNA-seq data GEO: GSE180532 31 N/A PBMC ATAC-Seq and RNA-seq data GEO: GSE297327 N/A Oligonucleotides Nextera Index kit Illumina 15055289 NEBNext multiplex oligos for Illumina, Dual Index Primers set 1 NEB E7600S GeoMx Immune Pathways panel Bruker (Nanostring) 121300201 Software and algorithms StrataQuest v7.1.1.1.143 TissueGnostics RRID:SCR_024861 CellProfiler Carpenter et al. 60 ; Ward et al. 61 RRID:SCR_007358 CytoMap Stoltzfus et al. 62 RRID:SCR_021227 FCS Express v7.18.0025 De Novo Software RRID:SCR_016431 GeoMx DSP software Bruker (Nanostring) N/A GraphPad Prism v9.5.1 www.GraphPad.com RRID:SCR_002798 ATAC-seq and RNA-seq analysis pipeline codes This paper at https://doi.org/10.5281/ zenodo.16575923 (https://github.com/ TheWhyofFry/ndhlovucellreports2025) and subsequent packages N/A TrimGalore Kundaje lab, Sloan et al. 63 N/A clusterProfiler Illumina, Yu et al. 64 RRID:SCR_016884 Diffbind and EdgeR Robinson et al. 65 RRID:SCR_012918; RRID:SCR_012802 ChIPSeeker Yu et al. 66 RRID:SCR_021322 Kallisto Bray et al. 67 RRID:SCR_016582 Ensembl version 85 (GRCh37) Dyer et al. 68 N/A Sleuth R package Pimentel et al. 69 RRID:SCR_016883 limma R package Ritchie et al. 70 RRID:SCR_010943 Correlation matrix codes This paper at https://doi.org/10.5281/ zenodo.16572491 (https://github.com/ AndreaO1125/Gex_corrplot) and https:// statsandr.com/blog/correlationcoefficient-and-correlation-test-in-r/ N/A R version 4.2.2 R: A Language and Environment for Statistical Computing 33 https://www.Rproject.org/ RRID:SCR_001905 Hmisc R package Harrell 35 https://CRAN.R-project.org/ package=Hmisc RRID:SCR_022947 Corrplot R package Wei and Simko 34 https://github.com/taiyun/ corrplot RRID:SCR_024683 FACS Diva BD RRID:SCR_001456 FlowJo 10.0.8 Flowjo LLC RRID:SCR_008520 UMAP plugin v4.1.1 McInnes et al. 71 N/A FlowSOM v2.6.0 Van Gassen et al. 72 RRID:SCR_016899 Flow cytometry UMAP codes This paper at https://doi.org/10.5281/ zenodo.16572922 (https://github.com/ AndreaO1125/T_cell_umaps) and subsequent packages N/A ggPlot2 R package Wickham 73 https://ggplot2.tidyverse.org RRID:SCR_014601 dplyr R package Wickham et al. 74 https://dplyr.tidyverse.org N/A 16 Cell Reports 44, 116181, September 23, 2025 ..
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