atac buffer b (10X Genomics)
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10X Genomics
atac buffer b
Atac Buffer B, 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/atac+buffer+b/atac+buffer/pmc13061643-300-9-12
Average 86 stars, based on 1 article reviews
Atac Buffer B, 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/atac+buffer+b/atac+buffer/pmc13061643-300-9-12
Average 86 stars, based on 1 article reviews
atac buffer b - by Bioz Stars,
2026-09
86/100 stars
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1) Product Images from "Single-nucleus epigenomic profiling of the adult human central nervous system unveils epigenetic memory of developmental programs"
Article Title: Single-nucleus epigenomic profiling of the adult human central nervous system unveils epigenetic memory of developmental programs
Journal: Nature Neuroscience
doi: 10.1038/s41593-026-02208-0
Figure Legend Snippet: a , Schematic for snATAC–seq and nanoCUT&Tag experiments in adult human CNS tissue. b , Two-dimensional UMAP of the snATAC dataset colored by clusters and labeled by cell type. c , Gene activity scores for different genes in the identified cell types. d , Two-dimensional UMAP of the H3K27ac nanoCUT&Tag dataset with cell annotations based on integration with snATAC–seq. e , Heatmap showing snATAC–seq differentially accessible peaks across different clusters and cell types. f , nanoCUT&Tag genome browser snapshot showing H3K27ac (top) and H3K27me3 (bottom) pseudobulk signal distribution across different marker genes for each cell type. g , nanoCUT&Tag meta-signal enrichment plots for H3K27ac (green) and H3K27me3 (red) in the MOL population. Top: line plots showing signal enrichment for the two modalities at different peak sets. Middle and bottom: heatmap showing H3K27ac (middle) and H3K27me3 (bottom) signal enrichment across different peak sets. Peak sets (left to right)—H3K27me3 peaks, H3K27ac peaks, ATAC peaks and ATAC peaks from a previously published dataset . h , Trimodal clustering of the genome highlights patterns of signal distribution across all cell types. i , Correlation matrix of ATAC, H3K27ac and H3K27me3 signals in each cell type shows strong correlation between active marks for individual cell types, and anticorrelation with the repressive H3K27me3. UMAP, uniform manifold approximation and projection; norm., normalized. Schematic in a created in BioRender; Castelo-Branco, G. https://biorender.com/orfbpyi (2025).
Techniques Used: Labeling, Activity Assay, Marker
Figure Legend Snippet: a , Cumulative distribution of the co-accessibility score for all loops identified by Cicero. Red line shows the score cutoff (0.5) used for assessing high-quality interactions and captures the top 5% of all loops. b , snATAC-seq genome browser snapshot showing chromatin accessibility signal in all cell types at CDC42EP1 locus (left), identified SOX10-distal enhancer (middle) and SOX10 locus (right) and the corresponding loops identified using Cicero. Red columns highlight the CDC42EP1 and SOX10 genes, and the gray column highlights the new enhancer. c , UCSC Genome Browser snapshot showing the identified enhancer locus (light blue column) as well as overlap with previously identified ENCODE cCREs, PhyloP base conservation score and evolutionary conservation with different species. d , snATAC-seq genome browser track showing chromatin accessibility in OPCs and MOLs at the newly identified enhancer, SOX10 locus, and previously characterized U1-U5, D6 and D7 enhancers (purple) and overlap with thyroid hormone receptor motifs (T3R, green) and TFAP2A motifs (orange). e , snATAC-seq and nanoCUT&Tag genome browser tracks the CDC42EP1-enhancer-SOX10 locus showing ATAC, H3K27ac and H3K27me3 pseudobulk signal in MOLs and OPCs and Cicero links. f , FACS plots showing transduction efficiency (left) and gene expression changes (qPCR) of SOX10 when directing dCas9–p300 to the U2 enhancer, U3 enhancer, and a nontargeting control (NTC) (right). N = 4 biological replicates; data shown as mean ± s.e.m. Statistics: one-way ANOVA with Tukey’s post hoc test. Two-sided t-test performed. *p ≤ 0.05, **p ≤ 0.01, ***p ≤ 0.001, NS = nonsignificant. g , Scatterplot showing TF strength of shared core TFs in MOLs (x axis) and OPCs (y axis) and highlighting the identified HOX genes. h , List of identified HOX genes being differentially accessible in spinal cord OPCs and MOLs. i , Scatterplot showing correlation between the multiome-RNA and multiome-ATAC. j , Stacked violin plot showing gene expression levels of all HOX genes in OPCs in all regions from an adult human brain transcriptomic atlas .
Techniques Used: Transduction, Gene Expression, Control
Figure Legend Snippet: a , Volcano plot showing differentially accessible peaks in SC and cortical OLGs. Previously characterized marker genes are shown in red and labeled. HOX cluster-associated peaks are shown in blue. Two-sided t test with Benjamini–Hochberg correction. Thresholds, adjusted P = 0.001, log(FC) = 1.5. b , Same as in a , but highlighting the specific HOX clusters identified as being differentially accessible. Two-sided t test with Benjamini–Hochberg correction. c , snATAC–seq genome browser snapshot showing pseudobulk chromatin accessibility signal in AST, MIGL, MOL and OPC populations from the CSC and motor cortex at the HOXA locus. MIGL signal is depleted in both regions, whereas AST, OPC and MOL exhibit accessibility in SC. d , Schematic showing workflow for the multiome experiment and UMAP embedding of the multiome ATAC with cell types annotated using the multiome-RNA. e , Stacked violin plots showing the expression (top) and promoter accessibility (bottom) in cortex and SC-derived MOLs and OPCs from a multiome experiment. Most differentially accessible HOX genes and OLG marker genes are shown. Schematic in d created in BioRender; Castelo-Branco, G. https://biorender.com/orfbpyi (2025).
Techniques Used: Marker, Labeling, Expressing, Derivative Assay
Figure Legend Snippet: a , nanoCUT&Tag and snATAC–seq genome browser tracks showing H3K27ac, H3K27me3 and ATAC pseudobulk signals in OLGs at the HOXA in CSC (upright track, darker shade) and motor cortex (inverted track, lighter shade). b , Same as in a , but for the HOXD locus. c , Gaussian smoothed normalized signal from ATAC (blue), H3K27ac (green) and H3K27me3 (red) across the HOXA cluster with a 50-kb flanking region upstream and downstream. Gray bars show the locations of the cumulative ‘signal boundaries’ identified in each modality. Color intensity reflects the cumulative strength of the signal boundary. d , Same as in c , but with each modality separated out. HOXA directionality is shown at the top, and arrows beneath show the medium (two modalities) and strong (three modalities) signal boundaries. e , nanoCUT&Tag and snATAC–seq genome browser track of the HOXA cluster showing the location of the strong signal boundaries and the corresponding inactive, primed and silenced chromatin domains. f , nanoCUT&Tag and snATAC–seq genome browser tracks showing the ATAC (blue), H3K27ac (green) and H3K27me3 (red) pseudobulk signal in the microglial and astrocyte populations at HOXD in both SC (CSC) and cortex (BA4). g , nanoCUT&Tag genome browser track around the HOXD locus (marked with dotted lines) with H3K27me3 (red) and H3K27ac (green) pseudobulk signal in SC OLGs. Single-cell tracks are shown below and sorted by decreasing H3K27me3 signal. Group 1 cells exhibit moderate H3K27me3 at the 3′ end, while group 2 cells show H3K27me3 depletion, and the amount of H3K27ac remains the same in both groups, suggesting that group 2 cells may be expressing low levels of HOX genes.
Techniques Used: Single Cell, Expressing
Figure Legend Snippet: a , snATAC-seq and nanoCUT&Tag genome browser tracks showing H3K27ac, H3K27me3 and ATAC pseudobulk signal in OLGs at the HOX-B and HOX-C clusters in cervical spinal cord (upright track, darker shade) and motor cortex (inverted track, lighter shade). Directionality of the clusters is shown by the arrow. b , Gaussian smoothed normalized signal from ATAC (blue), H3K27ac (green) and H3K27me3 (red) in spinal cord OLGs (solid line) and cortical OLGs (dotted line) across each HOX cluster with a 50 kb flanking region upstream and downstream. c , Gaussian smoothed normalized signal from ATAC (blue), H3K27ac (green) and H3K27me3 (red) across the HOXB, HOXC and HOXD clusters with a 50 kb flanking region upstream and downstream, separated by each modality. Gray bars show the location of ‘signal boundaries’ identified in each modality. Dotted lines mark the boundaries of each HOX cluster. Arrowheads underneath the plots mark intermediate and strong signal boundaries. HOX cluster directionality shown by arrow on top. d , snATAC-seq and nanoCUT&Tag genome browser tracks showing the ATAC (blue), H3K27ac (green), and H3K27me3 (red) pseudobulk signal in the microglial and astrocyte populations at HOXA in both spinal cord (CSC) and cortex (BA4).
Techniques Used:
Figure Legend Snippet: a , Normalized Micro-C contact matrix at 5-kb resolution at HOXA (left) and HOXD (right) loci and corresponding ATAC, H3K27ac and H3K27me3 tracks in human adult SC OLGs showing the c-Dom and t-Dom TAD structures, including the sub-TAD contacts. Contacts with distal enhancers is shown by the gray bars. b , Micro-C contact matrix showing contacts between HOX genes and flanking enhancers in hOPCs, in contrast to B cells. c , Correlation matrix of ATAC, H3K27ac and H3K27me3 signals in cortex and SC-derived OLGs across all four HOX clusters. d , Contact matrix showing long-range interaction between miR10b and LINC01116, virtual 4c (anchored on LINC01116) H3K27me3, H3K27ac, ATAC and inferred loops are shown. e , scATAC, H3K27ac and H3K27me3 tracks showing signal distribution at HOXD and distal LINC01116 in SC OLGs and cortex OLGs. f , Schematic showing plasmid and lentivirus setup for CRISPRi/a experiment. g , Gene expression changes (qPCR) of five genes from the CRISPRi/a experiment. Left, data from CRISPRa (left, dCas9–p300) and CRISPRi (right, dCas9–KRAB) targeting either miR10b (turquoise), LINC01116 (red) or an NTC (gray). n = 4 biological replicates; data shown as mean ± s.e.m.; statistics, one-way ANOVA with Tukey’s post hoc test; two-sided t test performed; * P ≤ 0.05, ** P ≤ 0.01, *** P ≤ 0.001. ANOVA, analysis of variance. Schematic in f created in BioRender; Castelo-Branco, G. https://biorender.com/orfbpyi (2025).
Techniques Used: Derivative Assay, Plasmid Preparation, Gene Expression
Figure Legend Snippet: a , Schematic of the adult human brain showing the location of pontine and thalamic gliomas along the A-P axis. Schematic in a created in BioRender. Castelo-branco, G. https://BioRender.com/orfbpyi (2025). b , snATAC-seq and nanoCUT&Tag normalized promoter accessibility (ATAC), H3K27ac and H3K27me3 signal in spinal cord OLGs (top) and cortical OLGs (bottom) at different developmental genes associated with brain and spinal cord patterning. c , Genome browser tracks showing nanoCUT&Tag H3K27ac and H3K27me3 pseudobulk signal coverage at the HOXA cluster in spinal cord (SC) derived adult human OLG (hOLG) and PFA-EP tumors, H3.3K27M pontine tumors, and H3.3K27M thalamic tumors . d , Same as c , but at the HOXD locus.
Techniques Used: Derivative Assay
Figure Legend Snippet: a , nanoCUT&Tag and snATAC–seq normalized promoter accessibility (ATAC), H3K27ac and H3K27me3 signal in SC OLGs (top) and cortical OLGs (bottom) at all HOX genes. Asterisk indicates the genes previously identified to be expressed in pontine HGGs . b , Normalized Hi–C contact matrix in H3.3K27M pontine HGG at the HOXA locus (marked by dotted lines) and corresponding ATAC, H3K27ac and H3K27me3 signals in SC OLGs and H3K27ac and H3K27me3 in H3.3K27M pontine HGG, showing similarity in mark distribution in nondiseased conditions and gliomas. c , Aggregate pileup analysis of hOPC loops (Micro-C) at HOXA (top) and HOXD (bottom) in pontine HGG, PFA-EP and thalamic HGG (left to right) . d , Insulation score from the Micro-C matrix across a 5-Mb window spanning HOXA (left) and HOXD (right) in the three HGGs (green, pink, yellow, from ref. ) and B cells (blue) overlaid on the hOPC insulation profile (black).
Techniques Used: Hi-C, Insulation
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