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atac seq libraries  (Zymo Research)


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    Zymo Research atac seq libraries
    Atac Seq Libraries, supplied by Zymo Research, used in various techniques. Bioz Stars score: 95/100, based on 73 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/atac+seq+libraries/ATAC-Seq/pmc13135392-269-0-7
    Average 95 stars, based on 73 article reviews
    atac seq libraries - by Bioz Stars, 2026-09
    95/100 stars

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    Related Articles

    Purification:

    Article Title: Arid1a-dependent canonical BAF complex suppresses inflammatory programs to drive efficient Germinal Center B cell responses
    Article Snippet: Nuclei were pelleted by centrifugation at 500g for 10 min at 4 °C, resuspended in 50 μL transposition mix (25 μL 2x TD buffer, 2.5 μL transposase (100 nM at final concentration), 16.5 μL PBS, 0.5 μL 1% digitonin, 0.5 μL10% Tween-20 and 5 μL H 2 O), and incubated at 37 °C for 30 min. DNA was purified using Zymo DNA Clean and Concentrator-5 cleanup kit (#D4013, Zymo Research) and, then was PCR amplified (11–12 cycles) using indexed oligos. .. The resulting ATAC-seq libraries were purified once again using the Zymo DNA Clean and Concentrator-5 cleanup kit and sequenced using an Illumina NovoSeq 6000 platform. ..

    Article Title: FOSL2 regulates endothelial cell state and chromatin accessibility in systemic sclerosis pulmonary vascular remodeling
    Article Snippet: .. ATAC-Seq libraries were then purified using the Zymo DNA Clean and Concentrator-5 kit and quantified using KAPA library quantification kit (Roche, KK4854). ..

    Generated:

    Article Title: Histone H3K9 Methyltransferases Regulate Cortical Growth by Coordinating Heterochromatin Formation and Neural Progenitor Dynamics
    Article Snippet: .. ATAC-seq libraries were generated using the Zymo-Seq ATAC Library Kit (Zymo, D5458) according to the manufacturer’s instructions. .. Library size distribution was assessed on a TapeStation 2200 (Agilent) before sequencing.

    Article Title: Early epigenetic priming of regeneration studied with a novel transgenic epigenetic reporter
    Article Snippet: .. ATAC-seq libraries were generated using the Zymo-Seq ATAC Library Kit (Zymo Research, cat. no. D5458). .. ATAC-seq libraries were generated using the Zymo-Seq ATAC Library Kit (Zymo Research, cat. no. D5458).

    Library Quantification:

    Article Title: FOSL2 regulates endothelial cell state and chromatin accessibility in systemic sclerosis pulmonary vascular remodeling
    Article Snippet: .. ATAC-Seq libraries were then purified using the Zymo DNA Clean and Concentrator-5 kit and quantified using KAPA library quantification kit (Roche, KK4854). ..



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    Stable mobilization of CEBPs and PPARG upon transient TAK-981 treatment in pre-adipocytes. ( A <t>)</t> <t>ATAC-seq</t> experimental layout in hTERT A41hWAT-SVF pre-adipocytes. Time series analysis and hierarchical clustering of significant variations in chromatin accessibility at day 0 (D0), 12 h (12h), and day (D7) after TAK-981 treatment. ( C ) GOBP analysis of ATAC-seq clusters 2 and 6 revealed in panel (B). See and for an analysis of all clusters. ( D – F ) Volcano plots displaying the results of ATAC-seq inferred differential TF activity analyses performed at D0, 12h, and D7 after TAK-981 or DMSO treatment. Colored dots indicate significant differentially mobilized TFs (TAK-981 versus DMSO). Differential binding score >0.05 and pAdj <0.001. ( G ) Time series analysis inferred TF activity over time (TAK-981 versus DMSO) at D0, 12h, and D7 after TAK-981 treatment. ( H ) Western blot analysis of CEBPB SUMOylation in DMSO and TAK-981-treated cells. ( I ) Western blot analysis of CEBPB and PPARG in DMSO, rosiglitazone, TAK-981-treated cells and cotreated hTERT A41hWAT-SVF pre-adipocytes. ( J ) Western blot analysis of PPARG in DMSO, rosiglitazone, TAK-981-treated cells and cotreated hASCs.
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    SOX2 directly activates immune modulatory programs in tSCs. A , MA plot showing the immune modulatory genes up-regulated following Sox2 overexpression (<3 fold) in PDV cells. Genes with significant differential expression (adjusted p-value < 0.05) are shown as pink dots. B , Venn diagrams illustrating the overlap between chromatin regions selectively accessible in tSCs and regions bound by SOX2, as determined by SOX2 CUT&RUN (CNR). C , Heatmap of IgG control CNR, SOX2 CNR, <t>and</t> <t>ATAC-seq</t> signals in tSCs and differentiated cells across all SOX2-bound chromatin regions. D , IGV images showing SOX2 CNR occupancy at representative immune modulatory gene loci.
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    Image Search Results


    Stable mobilization of CEBPs and PPARG upon transient TAK-981 treatment in pre-adipocytes. ( A ) ATAC-seq experimental layout in hTERT A41hWAT-SVF pre-adipocytes. Time series analysis and hierarchical clustering of significant variations in chromatin accessibility at day 0 (D0), 12 h (12h), and day (D7) after TAK-981 treatment. ( C ) GOBP analysis of ATAC-seq clusters 2 and 6 revealed in panel (B). See and for an analysis of all clusters. ( D – F ) Volcano plots displaying the results of ATAC-seq inferred differential TF activity analyses performed at D0, 12h, and D7 after TAK-981 or DMSO treatment. Colored dots indicate significant differentially mobilized TFs (TAK-981 versus DMSO). Differential binding score >0.05 and pAdj <0.001. ( G ) Time series analysis inferred TF activity over time (TAK-981 versus DMSO) at D0, 12h, and D7 after TAK-981 treatment. ( H ) Western blot analysis of CEBPB SUMOylation in DMSO and TAK-981-treated cells. ( I ) Western blot analysis of CEBPB and PPARG in DMSO, rosiglitazone, TAK-981-treated cells and cotreated hTERT A41hWAT-SVF pre-adipocytes. ( J ) Western blot analysis of PPARG in DMSO, rosiglitazone, TAK-981-treated cells and cotreated hASCs.

    Journal: Nucleic Acids Research

    Article Title: Transient SUMOylation inhibition in human pre-adipocytes stably imprints a transcriptional beiging fate

    doi: 10.1093/nar/gkag232

    Figure Lengend Snippet: Stable mobilization of CEBPs and PPARG upon transient TAK-981 treatment in pre-adipocytes. ( A ) ATAC-seq experimental layout in hTERT A41hWAT-SVF pre-adipocytes. Time series analysis and hierarchical clustering of significant variations in chromatin accessibility at day 0 (D0), 12 h (12h), and day (D7) after TAK-981 treatment. ( C ) GOBP analysis of ATAC-seq clusters 2 and 6 revealed in panel (B). See and for an analysis of all clusters. ( D – F ) Volcano plots displaying the results of ATAC-seq inferred differential TF activity analyses performed at D0, 12h, and D7 after TAK-981 or DMSO treatment. Colored dots indicate significant differentially mobilized TFs (TAK-981 versus DMSO). Differential binding score >0.05 and pAdj <0.001. ( G ) Time series analysis inferred TF activity over time (TAK-981 versus DMSO) at D0, 12h, and D7 after TAK-981 treatment. ( H ) Western blot analysis of CEBPB SUMOylation in DMSO and TAK-981-treated cells. ( I ) Western blot analysis of CEBPB and PPARG in DMSO, rosiglitazone, TAK-981-treated cells and cotreated hTERT A41hWAT-SVF pre-adipocytes. ( J ) Western blot analysis of PPARG in DMSO, rosiglitazone, TAK-981-treated cells and cotreated hASCs.

    Article Snippet: Samples for assay for transposase-accessible chromatin sequencing (ATAC-seq) were prepared based on previously published protocols with the Illumina ATAC-seq library preparation kit (20034197) [ – ].

    Techniques: Activity Assay, Binding Assay, Western Blot

    SOX2 directly activates immune modulatory programs in tSCs. A , MA plot showing the immune modulatory genes up-regulated following Sox2 overexpression (<3 fold) in PDV cells. Genes with significant differential expression (adjusted p-value < 0.05) are shown as pink dots. B , Venn diagrams illustrating the overlap between chromatin regions selectively accessible in tSCs and regions bound by SOX2, as determined by SOX2 CUT&RUN (CNR). C , Heatmap of IgG control CNR, SOX2 CNR, and ATAC-seq signals in tSCs and differentiated cells across all SOX2-bound chromatin regions. D , IGV images showing SOX2 CNR occupancy at representative immune modulatory gene loci.

    Journal: bioRxiv

    Article Title: Integrated analysis of stemness-associated immune modulatory circuits in squamous cell carcinomas

    doi: 10.64898/2026.04.02.716182

    Figure Lengend Snippet: SOX2 directly activates immune modulatory programs in tSCs. A , MA plot showing the immune modulatory genes up-regulated following Sox2 overexpression (<3 fold) in PDV cells. Genes with significant differential expression (adjusted p-value < 0.05) are shown as pink dots. B , Venn diagrams illustrating the overlap between chromatin regions selectively accessible in tSCs and regions bound by SOX2, as determined by SOX2 CUT&RUN (CNR). C , Heatmap of IgG control CNR, SOX2 CNR, and ATAC-seq signals in tSCs and differentiated cells across all SOX2-bound chromatin regions. D , IGV images showing SOX2 CNR occupancy at representative immune modulatory gene loci.

    Article Snippet: ATAC-seq libraries were sequenced on an Element Biosciences Aviti platform using paired-end reads.

    Techniques: Over Expression, Quantitative Proteomics, Control