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2026
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| Online Access: | https://doi.org/10.5281/zenodo.19478962 |
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| author | yang, shichao |
| author_facet | yang, shichao |
| contents | <p>Dataset Summary / Abstract:</p> <p>This dataset contains genome-wide chromatin accessibility and transcription factor occupancy profiles aimed at investigating the epigenetic mechanisms by which the Nuclear Factor Y (NF-Y) complex and the histone acetyltransferase coactivator Nej (CBP/p300) govern intestinal stem cell (ISC) quiescence and homeostasis in Drosophila melanogaster.</p> <p>The dataset comprises two complementary modalities:</p> <p>CUT&Tag profiling: Performed on single-cell suspensions derived from adult female Drosophila midguts to map the genome-wide binding landscapes of the NF-Y complex subunits. Using endogenously tagged lines (NF-YA-GFP and NF-YB-GFP) alongside an anti-GFP antibody, we captured high-resolution occupancy profiles. H3K4me3 profiling was included as a positive control for active promoter regions, and wild-type (w^1118^) midguts served as the negative control.</p> <p>ATAC-seq profiling: Performed on adult female midguts across three distinct genetic backgrounds to evaluate dynamic changes in chromatin accessibility associated with NF-Y loss and its dependence on Nej activity. The examined genotypes include control (w1118), progenitor-specific NF-YA knockdown (esgts > NF-YA-IR), and concurrent NF-YA and nej co-depletion (esgts > NF-YA-IR; nej-IR).</p> <p>Together, these integrated epignomic data provide direct physical and functional evidence demonstrating how the NF-Y complex constrains Nej-dependent chromatin accessibility at promoter-proximal regions of core proliferative pathways (such as the EGFR/MAPK cascade) to preserve intestinal homeostasis.</p> <p>Experimental Design & Protocols:</p> <p>Sample Characteristics: Dissected midguts from adult female Drosophila melanogaster (3-5 days post-eclosion for homeostatic/control lines; shifted to 29°C for indicated durations to induce transgenic RNAi expression).</p> <p>CUT&Tag Protocol: 30 midguts per sample were dissociated into single-cell suspensions via trypsinization, immobilized on Concanavalin A-coated magnetic beads, and incubated with primary antibodies (anti-GFP or anti-H3K4me3) followed by pAG-Tn5 transposition. Libraries were sequenced on the Illumina NovaSeq platform (Paired-End 150 bp).</p> <p>ATAC-seq Protocol: Freshly dissected midguts were enzymatically dissociated, permeabilized, and subjected to hyperactive Tn5 transposase-mediated tagmentation. Purified DNA fragments were amplified with indexed primers and sequenced on the Illumina NovaSeq platform (Paired-End 150 bp).</p> |
| format | Recurso digital |
| id | zenodo_https___doi_org_10_5281_zenodo_19478962 |
| institution | Zenodo |
| language | |
| publishDate | 2026 |
| publisher | Zenodo |
| record_format | zenodo |
| spellingShingle | ATAC-seq and cut&tag for NF-Y job yang, shichao <p>Dataset Summary / Abstract:</p> <p>This dataset contains genome-wide chromatin accessibility and transcription factor occupancy profiles aimed at investigating the epigenetic mechanisms by which the Nuclear Factor Y (NF-Y) complex and the histone acetyltransferase coactivator Nej (CBP/p300) govern intestinal stem cell (ISC) quiescence and homeostasis in Drosophila melanogaster.</p> <p>The dataset comprises two complementary modalities:</p> <p>CUT&Tag profiling: Performed on single-cell suspensions derived from adult female Drosophila midguts to map the genome-wide binding landscapes of the NF-Y complex subunits. Using endogenously tagged lines (NF-YA-GFP and NF-YB-GFP) alongside an anti-GFP antibody, we captured high-resolution occupancy profiles. H3K4me3 profiling was included as a positive control for active promoter regions, and wild-type (w^1118^) midguts served as the negative control.</p> <p>ATAC-seq profiling: Performed on adult female midguts across three distinct genetic backgrounds to evaluate dynamic changes in chromatin accessibility associated with NF-Y loss and its dependence on Nej activity. The examined genotypes include control (w1118), progenitor-specific NF-YA knockdown (esgts > NF-YA-IR), and concurrent NF-YA and nej co-depletion (esgts > NF-YA-IR; nej-IR).</p> <p>Together, these integrated epignomic data provide direct physical and functional evidence demonstrating how the NF-Y complex constrains Nej-dependent chromatin accessibility at promoter-proximal regions of core proliferative pathways (such as the EGFR/MAPK cascade) to preserve intestinal homeostasis.</p> <p>Experimental Design & Protocols:</p> <p>Sample Characteristics: Dissected midguts from adult female Drosophila melanogaster (3-5 days post-eclosion for homeostatic/control lines; shifted to 29°C for indicated durations to induce transgenic RNAi expression).</p> <p>CUT&Tag Protocol: 30 midguts per sample were dissociated into single-cell suspensions via trypsinization, immobilized on Concanavalin A-coated magnetic beads, and incubated with primary antibodies (anti-GFP or anti-H3K4me3) followed by pAG-Tn5 transposition. Libraries were sequenced on the Illumina NovaSeq platform (Paired-End 150 bp).</p> <p>ATAC-seq Protocol: Freshly dissected midguts were enzymatically dissociated, permeabilized, and subjected to hyperactive Tn5 transposase-mediated tagmentation. Purified DNA fragments were amplified with indexed primers and sequenced on the Illumina NovaSeq platform (Paired-End 150 bp).</p> |
| title | ATAC-seq and cut&tag for NF-Y job |
| url | https://doi.org/10.5281/zenodo.19478962 |