{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Anna Malkowska"],"organism":["Drosophila melanogaster"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-15696"],"description":["Targeted DamID of embryonic proliferating (epNSCs), quiescent (qNSCs) and larval proliferating neural stem cells (lpNSCs) was performed using worniu-GAL4, tubGAL80ts (for qNSCs and lpNSCs condition) or worniu-GAL4 (for epNSCs condition) as a driver to express nine different Dam-fusions and Dam on its own (Dam-Only) as control. The following Dam fusions were profiled: Dam-Brm, Dam-RNA Pol II, Dam-TAF3-phd (H3K4me3), Dam-Dnmt3a-pwwp (H3K36me3), Dam-15f11 (H4K20me1), Dam-19e5 (H3K9ac), Dam-HP1a, Dam-Pc, Dam-H1."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sample Collection - Targeted DamID of embryonic proliferating (epNSCs), quiescent (qNSCs) and larval proliferating neural stem cells (lpNSCs) was performed using worniu-GAL4, tubGAL80ts (for qNSCs and lpNSCs condition) or worniu-GAL4 (for epNSCs condition) as a driver to express nine different Dam-fusions and Dam on its own (Dam-Only) as control.","Library Construction - Library has been generated using a previously published DamID protocol (Marshall et al, 2016)","Nucleic Acid Extraction - DNA has been extracted from Drosophila melanogaster larvae according to a previous protocol (Southall et al, 2013, Marshall et al, 2016).","Sequencing - DNA DamID libraries were sequenced single-end, 100 cycles.","Sequencing - DNA DamID libraries were sequenced single-end, 50 cycles."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Sequence Alignment - Fastq files have been processed with damidseq_pipeline (Marshall et al, 2015) to align reads to dm6 genome with bowtie2 and extended them to the next GATC region.","Data Transformation - The aligned reads were used for broad peak calling with appropriate controls specified in the description using macs2. The peak calling and processing was performed using the damMer pipeline (Tang et al., 2022). Using the damMer_peaks.py script, the broadpeaks were merged, thresholded based on the FDR (10^-5) and filtered to only peaks found within 0.75 of the replicates, giving rise to reproPeak.bed processed files. reproPeaks were used to learn chromatin state model and generate genome annotations as described in the associated publication."],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Illumina HiSeq 1500","Illumina NovaSeq 6000"],"pubmed_abstract":["<h4>Summary</h4>  Homeostasis and repair of the nervous system is maintained by a population of resident neural stem cells (NSCs) retained in a state of reversible cell cycle arrest called quiescence. quiescent NSCs can resume proliferation in response to different physiological stimuli, such as diet or injury. Reactivation of NSCs requires changes in gene expression, much of which is regulated at the epigenomic level. We mapped, comprehensively and  in vivo , the dynamic epigenomic changes in NSC chromatin during stem cell quiescence and reactivation in  Drosophila . Contrary to expectations, we found that chromatin accessibility is increased in quiescent NSCs, remodelling extensively within both euchromatin and heterochromatin. Surprisingly, genes crucial for cell cycle progression are repressed whilst remaining within permissive H3K36me3-bound euchromatin. At the same time, genes necessary for cell-cell communication are derepressed by eviction of histone H1 and transition to a SWI/SNF-enriched active state. Our results reveal global expansion of accessible chromatin in quiescent NSCs without concomitant activation of transcription. Strikingly, this process reverses upon reactivation, indicating that opening of chromatin is a quiescence-specific event."],"study_type":["DNA-seq"],"species":["Drosophila melanogaster"],"pubmed_title":["Neural stem cell quiescence is actively maintained by the epigenome"],"pubmed_authors":["Andrea Brand","Anna Malkowska","Anna Malkowska, Jan Ander, Andrea H. Brand"],"additional_accession":[]},"is_claimable":false,"name":"Targeted DamID of selected chromatin proteins in quiescent and proliferating neural stem cells","description":"Targeted DamID of embryonic proliferating (epNSCs), quiescent (qNSCs) and larval proliferating neural stem cells (lpNSCs) was performed using worniu-GAL4, tubGAL80ts (for qNSCs and lpNSCs condition) or worniu-GAL4 (for epNSCs condition) as a driver to express nine different Dam-fusions and Dam on its own (Dam-Only) as control. The following Dam fusions were profiled: Dam-Brm, Dam-RNA Pol II, Dam-TAF3-phd (H3K4me3), Dam-Dnmt3a-pwwp (H3K36me3), Dam-15f11 (H4K20me1), Dam-19e5 (H3K9ac), Dam-HP1a, Dam-Pc, Dam-H1.","dates":{"release":"2025-11-11T00:00:00Z","modification":"2026-05-27T14:28:28.696Z","creation":"2025-10-10T13:19:36.098Z"},"accession":"E-MTAB-15696","cross_references":{"ENA":["ERP183309"],"EFO":["EFO_0002944","EFO_0004170","EFO_0002693","EFO_0004917","EFO_0005518","EFO_0003816","EFO_0004184"],"doi":["10.1101/2025.05.14.653490"]}}