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Series GSE163697 Query DataSets for GSE163697
Status Public on Aug 10, 2021
Title Decoding gene regulation in the fly brain
Organism Drosophila melanogaster
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary The Drosophila brain is a work horse in neuroscience.
Single-cell transcriptome analysis, 3D morphological classification, and detailed mapping of the connectome have revealed an immense diversity of neuronal and glial cell types that underlie the wide array of functional and behavioral traits in the fruit fly.
The developmental trajectories of each of these cell types, from neuroblast to mature neuron or glial cell, as well as their maintenance and plasticity in the adult brain, are controlled by gene regulatory networks (GRNs)
In this study, we profiled chromatin accessibility of 240,000 single cells, spanning nine developmental time points from larval, pupal, and adult brains, and integrated this data with single-cell transcriptomes.
This atlas reveals the regulatory connections between genomic enhancers and the single-cell transcriptomes for more than 80 cell types in the fly brain.
Each cell type is characterized by a unique chromatin accessibility landscape, with thousands of specific regulatory regions, summing to a total of 95,931 regulatory regions that are used in the brain.
Exploiting this resource, we find that the combination of expressed transcription factors is reflected by their respective motif architecture within cell type-specific enhancers.
 
Overall design snATAC-seq (10x Genomics CHROMIUM Single Cell ATAC Library & Gel Bead Kit v1) of fresh brains across development (2 replicates per time point for larvae and pupa, 7 replicates for adult including 2 central brain only) from genotype mixed Drosophila melanogaster (DGRP-551, DGRP-409, DGRP-502 and DGRP-639)
 
Contributor(s) Janssens J, Aibar S, Taskiran II, Aerts S
Citation(s) 34987221, 38086419
Submission date Dec 22, 2020
Last update date Feb 14, 2024
Contact name Stein Aerts
E-mail(s) [email protected]
Organization name KULeuven/VIB
Department Center for Brain & Disease Research
Lab S. Aerts Lab of Computational Biology
Street address Herestraat 49, bus 602
City LEUVEN
ZIP/Postal code 3000
Country Belgium
 
Platforms (3)
GPL19132 Illumina NextSeq 500 (Drosophila melanogaster)
GPL25244 Illumina NovaSeq 6000 (Drosophila melanogaster)
GPL30203 NextSeq 2000 (Drosophila melanogaster)
Samples (58)
GSM4984022 adult_brain_DGRP-551_Hyb-409-502_639_sample1
GSM4984023 adult_brain_DGRP-551_Hyb-409-502_639_sample2_2k
GSM4984024 adult_brain_DGRP-551_Hyb-409-502_639_sample3_4k
Relations
BioProject PRJNA687217
SRA SRP298930

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE163697_RAW.tar 726.7 Mb (http)(custom) TAR (of BW, NARROWPEAK)
GSE163697_bigwigs.tar.gz 1.9 Gb (ftp)(http) TAR
GSE163697_cisTopicObject_Adult.Rds.gz 736.8 Mb (ftp)(http) RDS
GSE163697_cisTopicObject_CB.Rds.gz 108.0 Mb (ftp)(http) RDS
GSE163697_cisTopicObject_Development.Rds.gz 461.1 Mb (ftp)(http) RDS
GSE163697_cisTopicObject_Glia.Rds.gz 88.2 Mb (ftp)(http) RDS
GSE163697_cisTopicObject_KC_T_Glia.Rds.gz 85.1 Mb (ftp)(http) RDS
GSE163697_cisTopicObject_OL.Rds.gz 121.1 Mb (ftp)(http) RDS
GSE163697_cisTopic_CB_Regions.RData.gz 11.8 Mb (ftp)(http) RDATA
GSE163697_cisTopic_Development_Regions.RData.gz 27.6 Mb (ftp)(http) RDATA
GSE163697_cisTopic_Glia_Regions.RData.gz 14.7 Mb (ftp)(http) RDATA
GSE163697_cisTopic_OL_Regions.RData.gz 12.8 Mb (ftp)(http) RDATA
GSE163697_consensus_peaks_500pb.bed.gz 1.8 Mb (ftp)(http) BED
GSE163697_ey_vs_repo.bw 19.0 Mb (ftp)(http) BW
GSE163697_final_peak_file_for_UAS-Dam-Mef2_x_R16A06-Gal4_2rep_FDR_0.01_with_peak_height_and_highest_associated_FDR.gff.gz 103.4 Kb (ftp)(http) GFF
GSE163697_final_peak_file_for_UAS-Dam-Mef2_x_R74G01-Gal4_2rep_FDR_0.01_with_peak_height_and_highest_assoiciated_FDR.gff.gz 118.0 Kb (ftp)(http) GFF
GSE163697_final_peak_file_for_UAS-Dam-acj6_x_atonal-Gal4_1rep_FDR_0.01_with_peak_height_and_highest_associated_FDR.gff.gz 132.2 Kb (ftp)(http) GFF
GSE163697_lolaN_repo_vs_elav_c3.0_common.bed.gz 179.4 Kb (ftp)(http) BED
GSE163697_lolaN_repo_vs_elav_c3.0_cond1.bed.gz 5.4 Kb (ftp)(http) BED
GSE163697_lolaN_repo_vs_elav_c3.0_cond2.bed.gz 4.4 Kb (ftp)(http) BED
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Processed data are available on Series record
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