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Series GSE141538 Query DataSets for GSE141538
Status Public on Feb 01, 2020
Title Zygotic pioneer factor activity of Odd-paired/Zic is necessary for establishing the Drosophila Segmentation Network
Organism Drosophila melanogaster
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Because chromatin determines whether information encoded in DNA is accessible to transcription factors, dynamic chromatin states in development may constrain how gene regulatory networks impart embryonic pattern. To determine the interplay between chromatin states and regulatory network function, we performed ATAC seq on Drosophila embryos over the period spanning the establishment of the segmentation network, comparing wild-type and mutant embryos in which all graded maternal patterning inputs are eliminated. While during the period between zygotic genome activation and gastrulation many regions maintain stable accessibility, cis-regulatory modules (CRMs) within the segmentation network undergo extensive patterning-dependent changes in accessibility. A component of the network, Odd-paired (opa), is necessary for pioneering accessibility of segmentation network CRMs. While opa is necessary to drive late opening of segmentation network cis-regulatory elements, competence for opa to pioneer is regulated over time. These results indicate that dynamic systems for chromatin regulation directly impact the interpretation of embryonic patterning information.
Overall design This study contains four distinct experiments. Experiment 1: ATAC-seq comparing wild-type and bicoid oskar capicua torsolike Toll[RM9] mutant embryos, staged either at 12 or 72 minutes into nuclear cycle 14. Three biological replicates (individual embryos) were collected per genotype and timepoint and subjected to ATAC library preparation. Samples were subjected to paired-end sequencing on an Illumina HiSeq2500 (2 x 63 bp reads). Experiment 2: ATAC-seq on a collection of embryos produced from a cross between opa[IIP32]/+ adults. Embryos were staged at 72 minutes into nuclear cycle 14. Twenty two embryos in total were collected and subjected to paired-end sequencing on an Illumina HiSeq 2500 (2 x 63 bp reads). Experiment 3: ChIP-seq for myc-tagged Opa. 200 cellular blastoderm stage embryos were collected from opa-myc homozygous adults and ChIPped with an anti-myc antibody. The control sample was an equivalent number of staged 'wild-type', i.e., not-myc-tagged embryos. The wild-type genotype is w[1118]. Three independent biological replicates were performed for experimental and control samples. ChIP-seq libraries were subjected to single-end sequencing on an Illumina HiSeq4000 (1 x 50 bp reads). Experiment 4: ATAC-seq comparing wild-type and maternal misexpression of odd-paired (tub>opa), staged at 12 minutes into nuclear cycle 13. Six biological replicates (individual embryos) were collected per genotype and subjected to ATAC library preparation. Samples were subjected to paired-end sequencing on an Illumina NextSeq500 (2 x 36bp reads).
Contributor(s) Blythe SA
Citation(s) 32347792
Submission date Dec 05, 2019
Last update date May 08, 2020
Contact name Shelby A Blythe
Organization name Northwestern University
Department Molecular Biosciences
Lab Blythe
Street address Northwestern University, Hogan Hall, 2205 Tech Drive
City Evanston
State/province IL
ZIP/Postal code 60208
Country USA
Platforms (3)
GPL17275 Illumina HiSeq 2500 (Drosophila melanogaster)
GPL19132 Illumina NextSeq 500 (Drosophila melanogaster)
GPL21306 Illumina HiSeq 4000 (Drosophila melanogaster)
Samples (51)
GSM4205792 wt_NC14_12_17091303
GSM4205793 wt_NC14_12_17091304
GSM4205794 wt_NC14_12_17091306
BioProject PRJNA593838
SRA SRP234892

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

Supplementary file Size Download File type/resource
GSE141538_Annotated_ATAC_Peaks_Tab_Delim.txt.gz 2.3 Mb (ftp)(http) TXT
GSE141538_Annotated_Opa_ChIP-seq_Tab_Delim.txt.gz 43.7 Kb (ftp)(http) TXT
GSE141538_Opa_myc_ChIP.wig.gz 25.1 Mb (ftp)(http) WIG 21.5 Mb (ftp)(http) WIG 22.5 Mb (ftp)(http) WIG 25.7 Mb (ftp)(http) WIG 25.7 Mb (ftp)(http) WIG
GSE141538_opa_mut_NC14_72.nucleoatac_signal.smooth.bedgraph.gz 70.4 Mb (ftp)(http) BEDGRAPH
GSE141538_opa_mut_NC14_72.nucleoatac_signal.smooth.bedgraph.gz.tbi.gz 23.2 Kb (ftp)(http) TBI
GSE141538_opa_mut_NC14_72.nucmap_combined.bed.gz 600.5 Kb (ftp)(http) BED
GSE141538_opa_mut_NC14_72.nucmap_combined.bed.gz.tbi.gz 18.1 Kb (ftp)(http) TBI 25.8 Mb (ftp)(http) WIG
GSE141538_opa_wt_NC14_72.nucleoatac_signal.smooth.bedgraph.gz 69.9 Mb (ftp)(http) BEDGRAPH
GSE141538_opa_wt_NC14_72.nucleoatac_signal.smooth.bedgraph.gz.tbi.gz 23.3 Kb (ftp)(http) TBI
GSE141538_opa_wt_NC14_72.nucmap_combined.bed.gz 571.0 Kb (ftp)(http) BED
GSE141538_opa_wt_NC14_72.nucmap_combined.bed.gz.tbi.gz 18.1 Kb (ftp)(http) TBI
GSE141538_tub-opa_NC13_12_open.wig.gz 17.9 Mb (ftp)(http) WIG
GSE141538_w_control_ChIP.wig.gz 25.1 Mb (ftp)(http) WIG
GSE141538_wt_NC13_12_open.wig.gz 19.1 Mb (ftp)(http) WIG
GSE141538_wt_NC14_12.nucleoatac_signal.smooth.bedgraph.gz 73.0 Mb (ftp)(http) BEDGRAPH
GSE141538_wt_NC14_12.nucleoatac_signal.smooth.bedgraph.gz.tbi.gz 23.4 Kb (ftp)(http) TBI
GSE141538_wt_NC14_12.nucmap_combined.bed.gz 595.6 Kb (ftp)(http) BED
GSE141538_wt_NC14_12.nucmap_combined.bed.gz.tbi.gz 18.1 Kb (ftp)(http) TBI 22.7 Mb (ftp)(http) WIG
GSE141538_wt_NC14_72.nucleoatac_signal.smooth.bedgraph.gz 70.5 Mb (ftp)(http) BEDGRAPH
GSE141538_wt_NC14_72.nucleoatac_signal.smooth.bedgraph.gz.tbi.gz 23.2 Kb (ftp)(http) TBI
GSE141538_wt_NC14_72.nucmap_combined.bed.gz 578.6 Kb (ftp)(http) BED
GSE141538_wt_NC14_72.nucmap_combined.bed.gz.tbi.gz 18.1 Kb (ftp)(http) TBI 23.3 Mb (ftp)(http) WIG
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