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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 67 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/atac-seq/pmc13135392-269-0-7?v=Zymo+Research
Average 95 stars, based on 67 article reviews

atac seq libraries - by Bioz Stars, 2026-07

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(A) Genome browser screenshot representing H3K4me3 and RNA pol II ChIP-seq signals in untreated cells (from and ) together with normalized ATAC-seq signals for individual replicates in each condition on a region of chromosome 17. (B) Heatmap representing normalized ATAC-seq signals for 80 DSBs on a 20 kb window (± 10 kb from the DSB) for individual replicates in each condition. (C) Average profiles of normalized ATAC-seq signal at 80 DSBs on a 4 kb window (± 2 kb from the DSB) in untreated cells (dark grey line), after 4 h of DSB induction (yellow line) or 24 h of DSB induction (red line) for replicate 1 (top panel) and replicate 2 (bottom panel). (D) Genome browser screenshot representing normalized ATAC-seq signals for a DSB located on chromosome 17 (DSB 526) at two different magnifications. Black arrows on the upper panel point to the decrease in accessibility proximal to the DSB and grey arrows on the lower panel point to distal increase in accessibility following DSB induction. (E) Average profiles of differential ATAC-seq represented as log2(+DSB/-DSB) after 4 h (yellow line) and 24 h (red line) of DSB induction at 80 DSBs on a 10 kb window (± 5 kb from the DSB) for replicate 1 (top panel) and replicate 2 (bottom panel). (F) Same as (E) on a 40 kb window (± 20 kb from the DSB). (G) Genome browser screenshot representing differential ATAC-seq profiles as log2(+DSB/-DSB) after 4 h or 24 h of DSB induction for a DSB located on chromosome 1 (DSB 526) together with ChIP-seq data for 53BP1 (blue), γH2AX (dark red), XRCC4 (grey) and BLESS (purple) signals (from , ). (H) Boxplot representing the distribution of ATAC-seq signal (Replicate 1) as log2(+DSB/-DSB) at 80 DSBs and 80 control regions after 4 h of DSB induction (yellow) or 24 h of DSB induction (red) on a 10 kb window (± 5 kb from the DSB), 40 kb window (± 20 kb from the DSB), 1 Mb window (± 500 kb from the DSB). Boxes show the interquartile range, center lines represent the median, whiskers extend by 1.5× IQR and dots represent individual outliers. P values were obtained from a two-sided Wilcoxon test.

Journal: bioRxiv

Article Title: Single-cell resolution of resection-dependent chromatin accessibility in response to DNA double strand breaks reveals specific gene expression programs

doi: 10.64898/2026.04.21.719635

Figure Lengend Snippet: (A) Genome browser screenshot representing H3K4me3 and RNA pol II ChIP-seq signals in untreated cells (from and ) together with normalized ATAC-seq signals for individual replicates in each condition on a region of chromosome 17. (B) Heatmap representing normalized ATAC-seq signals for 80 DSBs on a 20 kb window (± 10 kb from the DSB) for individual replicates in each condition. (C) Average profiles of normalized ATAC-seq signal at 80 DSBs on a 4 kb window (± 2 kb from the DSB) in untreated cells (dark grey line), after 4 h of DSB induction (yellow line) or 24 h of DSB induction (red line) for replicate 1 (top panel) and replicate 2 (bottom panel). (D) Genome browser screenshot representing normalized ATAC-seq signals for a DSB located on chromosome 17 (DSB 526) at two different magnifications. Black arrows on the upper panel point to the decrease in accessibility proximal to the DSB and grey arrows on the lower panel point to distal increase in accessibility following DSB induction. (E) Average profiles of differential ATAC-seq represented as log2(+DSB/-DSB) after 4 h (yellow line) and 24 h (red line) of DSB induction at 80 DSBs on a 10 kb window (± 5 kb from the DSB) for replicate 1 (top panel) and replicate 2 (bottom panel). (F) Same as (E) on a 40 kb window (± 20 kb from the DSB). (G) Genome browser screenshot representing differential ATAC-seq profiles as log2(+DSB/-DSB) after 4 h or 24 h of DSB induction for a DSB located on chromosome 1 (DSB 526) together with ChIP-seq data for 53BP1 (blue), γH2AX (dark red), XRCC4 (grey) and BLESS (purple) signals (from , ). (H) Boxplot representing the distribution of ATAC-seq signal (Replicate 1) as log2(+DSB/-DSB) at 80 DSBs and 80 control regions after 4 h of DSB induction (yellow) or 24 h of DSB induction (red) on a 10 kb window (± 5 kb from the DSB), 40 kb window (± 20 kb from the DSB), 1 Mb window (± 500 kb from the DSB). Boxes show the interquartile range, center lines represent the median, whiskers extend by 1.5× IQR and dots represent individual outliers. P values were obtained from a two-sided Wilcoxon test.

Article Snippet: For this, we performed single-nuclei ATAC-seq (10X Genomics, referred to as single-cell ATAC-seq for convenience) in untreated DIvA cells as well as following 4 hours and 24 hours of DSB induction to retrieve a total of more than 4000 cells (see Supplementary Table1).

Techniques: ChIP-sequencing, Control

Journal: bioRxiv

Article Title: Single-cell resolution of resection-dependent chromatin accessibility in response to DNA double strand breaks reveals specific gene expression programs

doi: 10.64898/2026.04.21.719635

Figure Lengend Snippet: (A) Genome browser screenshot representing signals for BLESS (purple), normalized ATAC-seq signals (Replicate 1, in black) as well as differential ATAC-seq profiles as log2(+DSB/-DSB) after 4 h or 24 h of DSB induction for a DSB located on chromosome 17 (DSB 343. Note that DSBs are numbered according to the predicted AsiSI sites in the genome, the majority of which are not cleaved efficiently, leading to discontinuous numbering between efficiently induced DSBs). (B) Same as (A), but for a DSB located on chromosome 1 (DSB 526). (C) Average differential ATAC-seq profile (Replicate 1) as log2(+DSB/-DSB) for 80 DSBs or 80 control regions on a 10 kb window (± 5 kb from the DSB) after 4 h of DSB induction (yellow, top panel) or 24 h of DSB induction (red, bottom panel). (D) Heatmap representing differential ATAC-seq profile (Replicate 1) as log2(+DSB/-DSB) for 80 DSBs on a 10 kb window (± 5 kb from the DSB) after 4h of DSB induction (left panel) or 24 h of DSB induction (right panel). (E) Same as (C) on a 40 kb window (± 20 kb from the DSB). (F) Same as (D) on a 40 kb window (± 20 kb from the DSB). (G) Genome browser screenshot representing differential ATAC-seq profiles as log2(+DSB/-DSB) after 4 h or 24 h of DSB induction as in , together with RPA ChIP seq in DIvA cells (blue), either untreated, treated for 4 h or 24 h and RAD51 ChIP-seq (dark red) for cells treated for 1 h, 4 h, or 24 h. Signals are displayed for a DSB located on chromosome 1 (DSB 526, left panel) and a DSB located on chromosome 17 (DSB 343, right panel). (H) Genome browser screenshot representing differential ATAC-seq profiles as log2(+DSB/-DSB) after 4 h or 24 h of DSB induction as in , XRCC4 ChIP-seq after 4 h and 24 h of DSB induction (from , in grey), RPA ChIP-seq after 4 h and 24 h of DSB induction (from in blue) and RAD51 ChIP-seq after 4 h and 24 h of DSB induction (from in dark red). Signals are displayed for a DSB located on chromosome 19 (DSB 432, left panel), a HR-prone DSB, and a DSB located on chromosome 11 (DSB 72, right panel), a NHEJ-prone DSB.

Techniques: Control, ChIP-sequencing

(A) Average profiles of differential ATAC-seq represented as log2(+DSB/-DSB) after 4 h (yellow lines) of DSB induction, overlayed with normalized ChIP-seq average profiles of MRE11 (dark pink, left panel), pATM (purple, middle left panel, from ), XRCC4 (grey, middle right panel, from ), and LIG4 (blue, right panel, from ) in untreated DIvA cells (dotted line), and after 4 h of DSB induction (solid line) at 80 DSBs on a 10 kb window (± 5 kb from the DSB). (B) Average profiles at 80 DSBs for differential ATAC-seq represented as log2(+DSB/-DSB) after 4 h (left panel, in yellow) and 24 h of DSB induction (right panel, in red), RPA ChIP-seq (blue) after 4 h (left panel) and 24 h (right panel) of DSB induction. Signals are displayed on a 20 kb window (± 10 kb from the DSB) for the 4 h time point (left panel) and 80 kb window (± 40 kb from the DSB) for the 24 h time point (right panel). (C) Average profiles at 80 DSBs for differential ATAC-seq represented as log2(+DSB/-DSB) after 4 h (left panel, in yellow) and 24 h of DSB induction (right panel, in red), RAD51 ChIP-seq (dark red) after 4 h (left panel) and 24 h (right panel) of DSB induction. Signals are displayed on a 20 kb window (± 10 kb from the DSB) for the 4 h time point (left panel) and 80 kb window (± 40 kb from the DSB) for the 24 h time point (right panel). (D) Average profiles for XRCC4, RPA and RAD51 ChIP-seq for 30 HR-prone DSBs and 30 NHEJ-prone DSBs as defined in after 4 h or 24 h of DSB induction. (E) Average profiles for differential ATAC-seq represented as log2(+DSB/-DSB) after 4 h (left panel) and 24 h of DSB induction (right panel) for 30 HR-prone DSBs (in red) and 30 NHEJ-prone DSBs (in yellow) as defined in . Signals are displayed on a 10 kb window (± 5 kb from the DSB). (F) Same as (E), but displayed on an 80 kb window (± 40 kb from the DSB). (G) Boxplot representing the distribution of ATAC-seq signal as log2(+DSB/-DSB) on a 4 kb window (± 2 kb from the DSB) and 20 kb window (± 10 kb from the DSB) for 30 HR-prone DSBs (in red) and 30 NHEJ-prone DSBs (in yellow) and 80 control regions (in grey) after 4 h and 24 h of DSB induction. Boxes show the interquartile range, center lines represent the median, whiskers extend by 1.5× IQR and dots represent individual outliers. P values were obtained from a two-sided Wilcoxon test. (H) Heatmap representation of CUT&Tag signals at 80 DSBs following 24 h of DSB induction (sorted by decreasing levels of differential ATAC-seq signals) on an 80 kb window (± 40 kb from the DSB) for IgG (negative control), ATM S1981P, RAD51 (with 2 different antibodies) and RPA S33P. (I) Same as (H) for IgG and RPA (with a change of scale compared to (E).

Journal: bioRxiv

Article Title: Single-cell resolution of resection-dependent chromatin accessibility in response to DNA double strand breaks reveals specific gene expression programs

doi: 10.64898/2026.04.21.719635

Figure Lengend Snippet: (A) Average profiles of differential ATAC-seq represented as log2(+DSB/-DSB) after 4 h (yellow lines) of DSB induction, overlayed with normalized ChIP-seq average profiles of MRE11 (dark pink, left panel), pATM (purple, middle left panel, from ), XRCC4 (grey, middle right panel, from ), and LIG4 (blue, right panel, from ) in untreated DIvA cells (dotted line), and after 4 h of DSB induction (solid line) at 80 DSBs on a 10 kb window (± 5 kb from the DSB). (B) Average profiles at 80 DSBs for differential ATAC-seq represented as log2(+DSB/-DSB) after 4 h (left panel, in yellow) and 24 h of DSB induction (right panel, in red), RPA ChIP-seq (blue) after 4 h (left panel) and 24 h (right panel) of DSB induction. Signals are displayed on a 20 kb window (± 10 kb from the DSB) for the 4 h time point (left panel) and 80 kb window (± 40 kb from the DSB) for the 24 h time point (right panel). (C) Average profiles at 80 DSBs for differential ATAC-seq represented as log2(+DSB/-DSB) after 4 h (left panel, in yellow) and 24 h of DSB induction (right panel, in red), RAD51 ChIP-seq (dark red) after 4 h (left panel) and 24 h (right panel) of DSB induction. Signals are displayed on a 20 kb window (± 10 kb from the DSB) for the 4 h time point (left panel) and 80 kb window (± 40 kb from the DSB) for the 24 h time point (right panel). (D) Average profiles for XRCC4, RPA and RAD51 ChIP-seq for 30 HR-prone DSBs and 30 NHEJ-prone DSBs as defined in after 4 h or 24 h of DSB induction. (E) Average profiles for differential ATAC-seq represented as log2(+DSB/-DSB) after 4 h (left panel) and 24 h of DSB induction (right panel) for 30 HR-prone DSBs (in red) and 30 NHEJ-prone DSBs (in yellow) as defined in . Signals are displayed on a 10 kb window (± 5 kb from the DSB). (F) Same as (E), but displayed on an 80 kb window (± 40 kb from the DSB). (G) Boxplot representing the distribution of ATAC-seq signal as log2(+DSB/-DSB) on a 4 kb window (± 2 kb from the DSB) and 20 kb window (± 10 kb from the DSB) for 30 HR-prone DSBs (in red) and 30 NHEJ-prone DSBs (in yellow) and 80 control regions (in grey) after 4 h and 24 h of DSB induction. Boxes show the interquartile range, center lines represent the median, whiskers extend by 1.5× IQR and dots represent individual outliers. P values were obtained from a two-sided Wilcoxon test. (H) Heatmap representation of CUT&Tag signals at 80 DSBs following 24 h of DSB induction (sorted by decreasing levels of differential ATAC-seq signals) on an 80 kb window (± 40 kb from the DSB) for IgG (negative control), ATM S1981P, RAD51 (with 2 different antibodies) and RPA S33P. (I) Same as (H) for IgG and RPA (with a change of scale compared to (E).

Techniques: ChIP-sequencing, Control, Negative Control

(A) Western blots of CtIP and ɑ-Tubulin after control or CtIP knockdown in U2OS-DIvA cells. (B) Boxplot representing the distribution of differential ATAC-seq profiles as log2(+DSB/-DSB) for 80 DSBs after 4 h or 24 h of DSB induction in siControl- or si-CtIP-treated cells on a 4 kb window (± 2 kb from the DSB, left panel) and 20 kb window (± 10 kb from the DSB, right panel). Boxes show the interquartile range, center lines represent the median, whiskers extend by 1.5× IQR and dots represent individual outliers. P values were obtained from a paired two-sided Wilcoxon test. (C) Boxplot representing the distribution of differential ATAC-seq profiles as log2(+DSB/-DSB) for 80 DSBs after 4 h or 24 h of DSB induction and with additional treatment of inhibitors of MRE11 endonuclease activity (PFM01), ATM (KU-55933), and DNA-PKcs (NU7441) on a 4 kb window (± 2 kb from the DSB, left panel) and 20 kb window (± 10 kb from the DSB, right panel). Boxes show the interquartile range, center lines represent the median, whiskers extend by 1.5× IQR and dots represent individual outliers. P values were obtained from a paired two-sided Wilcoxon test. (D) Western blots of EXO1 (top panel), DNA2 (bottom panel), and ɑ-Tubulin after control or combined EXO1 and DNA2 knockdown in U2OS-DIvA cells. (E) Boxplot representing the distribution of differential ATAC-seq profiles as log2(+DSB/-DSB) for 80 DSBs after 4 h or 24 h of DSB induction in siControl- or siEXO1+DNA2-treated cells on a 4 kb window (± 2 kb from the DSB, left panel) and 20 kb window (± 10 kb from the DSB, right panel). Boxes show the interquartile range, center lines represent the median, whiskers extend by 1.5× IQR and dots represent individual outliers. P values were obtained from a paired two-sided Wilcoxon test. (F) DSBs were induced in DIvA cells for 24 h upon concomitant treatment with the following inhibitors: MRE11i (Mirin, 100 μM), DNA-PKi (NU7441, 2 μM), ATMi (KU-55933, 20 μM) and RAD51i (B02, 25 μM) as indicated. Cells were stained with γH2AX and RAD51 antibodies and representative images are shown. (G) Quantification of RAD51 foci number (left panel) and total foci area (right panel) following treatments described in (I). (H) Boxplot representing the distribution of differential ATAC-seq profiles as log2(+DSB/-DSB) for 80 DSBs after 4 h or 24 h of DSB induction and with additional treatment of inhibitors of RAD51 (B02), MRE11 exonuclease activity (Mirin), and DNA-PKcs (NU7441) on a 4 kb window (± 2 kb from the DSB, left panel) and 20 kb window (± 10 kb from the DSB, right panel). Boxes show the interquartile range, center lines represent the median, whiskers extend by 1.5× IQR and dots represent individual outliers. P values were obtained from a paired two-sided Wilcoxon test. (I) Same as (H) on a 10 kb window (± 5 kb from the DSB) with the central 2 kb (± 1 kb from the DSB) removed (left panel), and on a 20 kb window (± 10 kb from the DSB) with the central 2 kb (± 1 kb from the DSB) removes (right panel).

Journal: bioRxiv

Article Title: Single-cell resolution of resection-dependent chromatin accessibility in response to DNA double strand breaks reveals specific gene expression programs

doi: 10.64898/2026.04.21.719635

Figure Lengend Snippet: (A) Western blots of CtIP and ɑ-Tubulin after control or CtIP knockdown in U2OS-DIvA cells. (B) Boxplot representing the distribution of differential ATAC-seq profiles as log2(+DSB/-DSB) for 80 DSBs after 4 h or 24 h of DSB induction in siControl- or si-CtIP-treated cells on a 4 kb window (± 2 kb from the DSB, left panel) and 20 kb window (± 10 kb from the DSB, right panel). Boxes show the interquartile range, center lines represent the median, whiskers extend by 1.5× IQR and dots represent individual outliers. P values were obtained from a paired two-sided Wilcoxon test. (C) Boxplot representing the distribution of differential ATAC-seq profiles as log2(+DSB/-DSB) for 80 DSBs after 4 h or 24 h of DSB induction and with additional treatment of inhibitors of MRE11 endonuclease activity (PFM01), ATM (KU-55933), and DNA-PKcs (NU7441) on a 4 kb window (± 2 kb from the DSB, left panel) and 20 kb window (± 10 kb from the DSB, right panel). Boxes show the interquartile range, center lines represent the median, whiskers extend by 1.5× IQR and dots represent individual outliers. P values were obtained from a paired two-sided Wilcoxon test. (D) Western blots of EXO1 (top panel), DNA2 (bottom panel), and ɑ-Tubulin after control or combined EXO1 and DNA2 knockdown in U2OS-DIvA cells. (E) Boxplot representing the distribution of differential ATAC-seq profiles as log2(+DSB/-DSB) for 80 DSBs after 4 h or 24 h of DSB induction in siControl- or siEXO1+DNA2-treated cells on a 4 kb window (± 2 kb from the DSB, left panel) and 20 kb window (± 10 kb from the DSB, right panel). Boxes show the interquartile range, center lines represent the median, whiskers extend by 1.5× IQR and dots represent individual outliers. P values were obtained from a paired two-sided Wilcoxon test. (F) DSBs were induced in DIvA cells for 24 h upon concomitant treatment with the following inhibitors: MRE11i (Mirin, 100 μM), DNA-PKi (NU7441, 2 μM), ATMi (KU-55933, 20 μM) and RAD51i (B02, 25 μM) as indicated. Cells were stained with γH2AX and RAD51 antibodies and representative images are shown. (G) Quantification of RAD51 foci number (left panel) and total foci area (right panel) following treatments described in (I). (H) Boxplot representing the distribution of differential ATAC-seq profiles as log2(+DSB/-DSB) for 80 DSBs after 4 h or 24 h of DSB induction and with additional treatment of inhibitors of RAD51 (B02), MRE11 exonuclease activity (Mirin), and DNA-PKcs (NU7441) on a 4 kb window (± 2 kb from the DSB, left panel) and 20 kb window (± 10 kb from the DSB, right panel). Boxes show the interquartile range, center lines represent the median, whiskers extend by 1.5× IQR and dots represent individual outliers. P values were obtained from a paired two-sided Wilcoxon test. (I) Same as (H) on a 10 kb window (± 5 kb from the DSB) with the central 2 kb (± 1 kb from the DSB) removed (left panel), and on a 20 kb window (± 10 kb from the DSB) with the central 2 kb (± 1 kb from the DSB) removes (right panel).

Techniques: Western Blot, Control, Knockdown, Activity Assay, Staining

(A) Genome browser screenshot representing differential ATAC-seq profiles as log2(+DSB/-DSB) after 4 h or 24 h of DSB induction in siControl- or siCtIP-treated cells for a DSB located on chromosome 1 (DSB 526). (B) Average profiles of differential ATAC-seq represented as log2(+DSB/-DSB) in siControl-treated cells after 4 h (yellow line, left panel) and 24 h (red line, right panel) of DSB induction, and in siCtIP-treated cells after 4 h (light purple, left panel) and 24 h (dark purple, right panel) at 80 DSBs on a 10 kb window (± 5 kb from the DSB, left panel) and on a 40 kb window (± 20 kb from the DSB, right panel). (C) Genome browser screenshot representing differential ATAC-seq profiles as log2(+DSB/-DSB) after 4 h or 24 h of DSB induction, as well in cells with additional treatment of inhibitors of MRE11 endonuclease activity (PFM01), ATM (KU-55933), and DNA-PKcs (NU7441) for a DSB located on chromosome 1 (DSB 526). (D) Average profiles of differential ATAC-seq represented as log2(+DSB/-DSB) in cells after 4 h (yellow line) of DSB induction, and in cells with additional treatment of inhibitors of MRE11 endonuclease activity (PFM01, blue line), and ATM (KU-55933, purple line,) at 80 DSBs on a 10 kb window (± 5 kb from the DSB). (E) Average profiles of differential ATAC-seq represented as log2(+DSB/-DSB) in cells after 24 h (red line) of DSB induction, and in cells with additional treatment of inhibitors of MRE11 endonuclease activity (PFM01, blue line), ATM (KU-55933, purple line), and DNA-PKcs (NU7441, grey line), at 80 DSBs on a 40 kb window (± 20 kb from the DSB). (F) Genome browser screenshot representing differential ATAC-seq profiles as log2(+DSB/-DSB) after 4 h or 24 h of DSB induction in siControl- or siEXO1+DNA2-treated cells for a DSB located on chromosome 1 (DSB 526). (G) Average profiles of differential ATAC-seq represented as log2(+DSB/-DSB) in siControl-treated cells after 4 h (yellow line, left panel) and 24 h (red line, right panels) of DSB induction, and in siEXO1+DNA2-treated cells after 4 h (light pink, left panel) and 24 h (light purple, right panels) at 80 DSBs on a 10 kb window (± 5 kb from the DSB, left panel) and on a 40 kb window (± 20 kb from the DSB, right panel). (H) Genome browser screenshot representing differential ATAC-seq profiles as log2(+DSB/-DSB) after 24 h of DSB induction, as well in cells with additional treatment of inhibitors of MRE11 exonuclease activity (Mirin), DNA-PKcs (NU7441), and RAD51 (B02) for a DSB located on chromosome 1 (DSB 526). (I) Average profiles of differential ATAC-seq represented as log2(+DSB/-DSB) in cells after 24 h (red lines) of DSB induction, and in cells with additional treatment of inhibitors of RAD51 (B02, black line, left panel), MRE11 exonuclease activity (Mirin, teal line, middle panel), and DNA-PKcs (NU7441, grey line, right panel), at 80 DSBs on a 40 kb window (± 20 kb from the DSB).

Journal: bioRxiv

Article Title: Single-cell resolution of resection-dependent chromatin accessibility in response to DNA double strand breaks reveals specific gene expression programs

doi: 10.64898/2026.04.21.719635

Figure Lengend Snippet: (A) Genome browser screenshot representing differential ATAC-seq profiles as log2(+DSB/-DSB) after 4 h or 24 h of DSB induction in siControl- or siCtIP-treated cells for a DSB located on chromosome 1 (DSB 526). (B) Average profiles of differential ATAC-seq represented as log2(+DSB/-DSB) in siControl-treated cells after 4 h (yellow line, left panel) and 24 h (red line, right panel) of DSB induction, and in siCtIP-treated cells after 4 h (light purple, left panel) and 24 h (dark purple, right panel) at 80 DSBs on a 10 kb window (± 5 kb from the DSB, left panel) and on a 40 kb window (± 20 kb from the DSB, right panel). (C) Genome browser screenshot representing differential ATAC-seq profiles as log2(+DSB/-DSB) after 4 h or 24 h of DSB induction, as well in cells with additional treatment of inhibitors of MRE11 endonuclease activity (PFM01), ATM (KU-55933), and DNA-PKcs (NU7441) for a DSB located on chromosome 1 (DSB 526). (D) Average profiles of differential ATAC-seq represented as log2(+DSB/-DSB) in cells after 4 h (yellow line) of DSB induction, and in cells with additional treatment of inhibitors of MRE11 endonuclease activity (PFM01, blue line), and ATM (KU-55933, purple line,) at 80 DSBs on a 10 kb window (± 5 kb from the DSB). (E) Average profiles of differential ATAC-seq represented as log2(+DSB/-DSB) in cells after 24 h (red line) of DSB induction, and in cells with additional treatment of inhibitors of MRE11 endonuclease activity (PFM01, blue line), ATM (KU-55933, purple line), and DNA-PKcs (NU7441, grey line), at 80 DSBs on a 40 kb window (± 20 kb from the DSB). (F) Genome browser screenshot representing differential ATAC-seq profiles as log2(+DSB/-DSB) after 4 h or 24 h of DSB induction in siControl- or siEXO1+DNA2-treated cells for a DSB located on chromosome 1 (DSB 526). (G) Average profiles of differential ATAC-seq represented as log2(+DSB/-DSB) in siControl-treated cells after 4 h (yellow line, left panel) and 24 h (red line, right panels) of DSB induction, and in siEXO1+DNA2-treated cells after 4 h (light pink, left panel) and 24 h (light purple, right panels) at 80 DSBs on a 10 kb window (± 5 kb from the DSB, left panel) and on a 40 kb window (± 20 kb from the DSB, right panel). (H) Genome browser screenshot representing differential ATAC-seq profiles as log2(+DSB/-DSB) after 24 h of DSB induction, as well in cells with additional treatment of inhibitors of MRE11 exonuclease activity (Mirin), DNA-PKcs (NU7441), and RAD51 (B02) for a DSB located on chromosome 1 (DSB 526). (I) Average profiles of differential ATAC-seq represented as log2(+DSB/-DSB) in cells after 24 h (red lines) of DSB induction, and in cells with additional treatment of inhibitors of RAD51 (B02, black line, left panel), MRE11 exonuclease activity (Mirin, teal line, middle panel), and DNA-PKcs (NU7441, grey line, right panel), at 80 DSBs on a 40 kb window (± 20 kb from the DSB).

Techniques: Activity Assay

Journal: bioRxiv

Article Title: Single-cell resolution of resection-dependent chromatin accessibility in response to DNA double strand breaks reveals specific gene expression programs

doi: 10.64898/2026.04.21.719635

Figure Lengend Snippet: (A) Pseudo-bulk average differential ATAC-seq profile as log2(+DSB/-DSB) for 80 DSBs after 4 h of DSB induction on a 10 kb window (± 5 kb from the DSB). (B) Single-cell differential chromatin accessibility profiles as log2(+DSB/-DSB) (n=300 cells) on a 10 kb window (± 5 kb from the DSB) after 4 h of DSB induction for DSBs 526, 379, and 1129. (C) Same as (B), for DSB 72. (D) Violin plots showing average gene set scores per cell for S phase and G2/M phase marker gene sets as defined in Seurat in cells after 4 h of DSB induction. (E) Pseudo-bulk average differential ATAC-seq profile as log2(+DSB/-DSB) for cells in G1 (blue line), S (pink line) or G2/M (gold line) for 80 DSBs after 4 h of DSB induction on a 10 kb window (± 5 kb from the DSB). (F) Single-cell differential chromatin accessibility profiles as log2(+DSB/-DSB) for cells in G1, S or G2/M on a 10 kb window (± 5 kb from the DSB) after 4 h of DSB induction for DSBs 526 and 379. (G) Same as (F), for DSB 72. (H) Single-cell differential chromatin accessibility profiles as log2(+DSB/-DSB) for cells in G1, S or G2/M on a 40 kb window (± 20 kb from the DSB) after 24 h of DSB induction for DSBs 533, 392, and 199 (I) Single-cell differential chromatin accessibility profiles as log2(+DSB/-DSB) (n=300 cells) on a 40 kb window (± 20 kb from the DSB) after 24 h of DSB induction for DSB 526, 343, and 533, with normalized ATAC-seq coverage tracks (black) in untreated cells highlighting accessible genomic regions (in grey). (J) Single-cell differential chromatin accessibility profiles as log2(+DSB/-DSB) for cells after 24 h of DSB induction on an 80 kb window for DSB 533 (n=106 cells). Cells ordered by calculated upstream-to-downstream ratio (see methods). (K) Same as (J), for DSB 600 (n=72 cells). (L) Boxplot representing the upstream-to-downstream ratio (see methods) per cell at individual HR-prone DSBs after 24 h of DSB induction. Boxes show the interquartile range, center lines represent the median, whiskers extend by 1.5× IQR and dots represent individual outliers. (M) Barplot representing the absolute Z-score of the upstream-to-downstream ratio of individual HR-prone DSBs after 24 h of DSB induction. (N) Same as (J), for DSB 343 (n=62 cells).

Techniques: Single Cell, Marker

Journal: bioRxiv

Article Title: Single-cell resolution of resection-dependent chromatin accessibility in response to DNA double strand breaks reveals specific gene expression programs

doi: 10.64898/2026.04.21.719635

Figure Lengend Snippet: (A) Pseudo-bulk average differential ATAC-seq profile as log2(+DSB/-DSB) for 80 DSBs after 24 h of DSB induction on a 10 kb window (± 5 kb from the DSB, top panel) and 40 kb window (± 20 kb from the DSB, bottom panel). (B) Single-cell differential chromatin accessibility profiles as log2(+DSB/-DSB) (n=300 cells) on an 80 kb window (± 40 kb from the DSB) after 24 h of DSB induction for DSBs 526, 379, 1129, 343, 533, and 495. (C) Same as (B), for DSBs 72 and 199. (D) Violin plots showing average gene set scores per cell for S phase and G2/M phase marker gene sets as defined in Seurat in cells after 24 h of DSB induction. (E) Pseudo-bulk average differential ATAC-seq profile as log2(+DSB/-DSB) for cells in G1 (blue line), S (pink line) or G2/M (gold line) for 80 DSBs after 24 h of DSB induction on a 40 kb window (± 20 kb from the DSB). (F) Single-cell differential chromatin accessibility profiles as log2(+DSB/-DSB) for cells in G1, S or G2/M on a 40 kb window (± 20 kb from the DSB) after 24 h of DSB induction for DSBs 526 and 379. (G) Same as (F), for DSB 72 (H) Single-cell differential chromatin accessibility profiles as log2(+DSB/-DSB) for cells after 24 h of DSB induction on an 80kb window for DSBs 379 (n=151 cells) and 526 (n=100 cells). Cells ordered by calculated upstream-to-downstream ratio (see methods). (I) Same as (H) for DSBs 495 (n=52 cells) and 1129 (n=74 cells). (J) Same as (J) for DSBs 608 (n=56 cells) and 765 (n=78 cells).

Techniques: Single Cell, Marker

(A) Pseudo-bulk average differential ATAC-seq profiles from scMultiome as log2(+DSB/-DSB) at 80 DSBs for cells after 4 h (top panel) and 24 h (middle panel) of DSB induction, as well in cells with additional treatment of inhibitors of MRE11 exonuclease activity (Mirin, bottom panel) on a 10 kb window (± 5 kb from the DSB, top panel) and a 40 kb window (± 20 kb from the DSB, middle and bottom panels). (B) Dot plots representing the activity of all assessed Hallmark (H), GO, and Pathcards (PC) gene signatures per treatment from scMultiome. The size of the dot reflects the percentage of cells expressing the genes of interest while the color bar encodes for up- or down-regulation compared with untreated cells. (C) Enrichment of Hallmark gene sets from 286 significantly upregulated genes after 4h of DSB induction identified from bulk RNA-seq experiments . The x-axis shows the gene ratio (number of genes in the term divided by total input genes). The dot size represents the number of genes associated with each term, and the color indicates the adjusted P value (Benjamini–Hochberg FDR), with darker colors corresponding to higher significance. (D) Dot plots representing the activity of all assessed Hallmark (H), GO, and Pathcards (PC) gene signatures per treatment from scRNA-seq. The size of the dot reflects the percentage of cells expressing the genes of interest while the color bar encodes for up- or down-regulation compared with untreated cells. (E) Boxplot representing the number of ɣH2AX foci detected by immunofluorescence in U2OS-DIvA cells following the indicated treatment for 4 h. Boxes show the interquartile range, center lines represent the median, whiskers extend by 1.5× IQR and dots represent individual outliers. (F) UMAP projection of 8032 single-cell gene expression profiles from scMultiome. Cells colored according to individual treatments. (G) Same as (F), with individual UMAP projections for each treatment.

Journal: bioRxiv

Article Title: Single-cell resolution of resection-dependent chromatin accessibility in response to DNA double strand breaks reveals specific gene expression programs

doi: 10.64898/2026.04.21.719635

Figure Lengend Snippet: (A) Pseudo-bulk average differential ATAC-seq profiles from scMultiome as log2(+DSB/-DSB) at 80 DSBs for cells after 4 h (top panel) and 24 h (middle panel) of DSB induction, as well in cells with additional treatment of inhibitors of MRE11 exonuclease activity (Mirin, bottom panel) on a 10 kb window (± 5 kb from the DSB, top panel) and a 40 kb window (± 20 kb from the DSB, middle and bottom panels). (B) Dot plots representing the activity of all assessed Hallmark (H), GO, and Pathcards (PC) gene signatures per treatment from scMultiome. The size of the dot reflects the percentage of cells expressing the genes of interest while the color bar encodes for up- or down-regulation compared with untreated cells. (C) Enrichment of Hallmark gene sets from 286 significantly upregulated genes after 4h of DSB induction identified from bulk RNA-seq experiments . The x-axis shows the gene ratio (number of genes in the term divided by total input genes). The dot size represents the number of genes associated with each term, and the color indicates the adjusted P value (Benjamini–Hochberg FDR), with darker colors corresponding to higher significance. (D) Dot plots representing the activity of all assessed Hallmark (H), GO, and Pathcards (PC) gene signatures per treatment from scRNA-seq. The size of the dot reflects the percentage of cells expressing the genes of interest while the color bar encodes for up- or down-regulation compared with untreated cells. (E) Boxplot representing the number of ɣH2AX foci detected by immunofluorescence in U2OS-DIvA cells following the indicated treatment for 4 h. Boxes show the interquartile range, center lines represent the median, whiskers extend by 1.5× IQR and dots represent individual outliers. (F) UMAP projection of 8032 single-cell gene expression profiles from scMultiome. Cells colored according to individual treatments. (G) Same as (F), with individual UMAP projections for each treatment.

Techniques: Activity Assay, Expressing, RNA Sequencing, Immunofluorescence, Single Cell, Gene Expression

(A) UMAP projection of 10397 single-cell gene expression profiles from scMultiome experiments. Cells colored according to individual treatments. (B) Same as (A), with individual UMAP projections for each treatment. (C) Same as (A), cells colored according to identified clusters. (D) Same as (C), with individual UMAP projections for each treatment. (E) Dot plots representing the average activity of Pathcards (PC) and GO gene signatures per identified cluster relating to a specific treatment. The size of the dot reflects the percentage of cells expressing the genes of interest while the color bar encodes for up- or down-regulation compared with untreated cells. (F) Histogram representing the percentage of cells in each cell cycle phase per identified cluster relating to a specific treatment. (G) Pseudo-bulk average differential ATAC-seq profiles as log2(+DSB/-DSB) at 80 DSBs for cells in each identified cluster relating to a specific treatment (clusters 0, 1, and 2 on the left panel, clusters 4 and 6 on the middle panel, clusters 3 and 5 on the right panel) on a 10 kb window (± 5 kb from the DSB, left panel) and 40 kb window (± 20 kb from the DSB, middle and right panels). (H) UMAP projections of cells annotated by cell cycle phase (left panel) and cluster identity (right panel) with overlaid trajectory paths representing pseudotime inference highlighting potential cellular transitions across clusters.

Journal: bioRxiv

Article Title: Single-cell resolution of resection-dependent chromatin accessibility in response to DNA double strand breaks reveals specific gene expression programs

doi: 10.64898/2026.04.21.719635

Figure Lengend Snippet: (A) UMAP projection of 10397 single-cell gene expression profiles from scMultiome experiments. Cells colored according to individual treatments. (B) Same as (A), with individual UMAP projections for each treatment. (C) Same as (A), cells colored according to identified clusters. (D) Same as (C), with individual UMAP projections for each treatment. (E) Dot plots representing the average activity of Pathcards (PC) and GO gene signatures per identified cluster relating to a specific treatment. The size of the dot reflects the percentage of cells expressing the genes of interest while the color bar encodes for up- or down-regulation compared with untreated cells. (F) Histogram representing the percentage of cells in each cell cycle phase per identified cluster relating to a specific treatment. (G) Pseudo-bulk average differential ATAC-seq profiles as log2(+DSB/-DSB) at 80 DSBs for cells in each identified cluster relating to a specific treatment (clusters 0, 1, and 2 on the left panel, clusters 4 and 6 on the middle panel, clusters 3 and 5 on the right panel) on a 10 kb window (± 5 kb from the DSB, left panel) and 40 kb window (± 20 kb from the DSB, middle and right panels). (H) UMAP projections of cells annotated by cell cycle phase (left panel) and cluster identity (right panel) with overlaid trajectory paths representing pseudotime inference highlighting potential cellular transitions across clusters.

Techniques: Single Cell, Gene Expression, Activity Assay, Expressing

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