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Series GSE152770 Query DataSets for GSE152770
Status Public on Mar 03, 2021
Title GAF is essential for zygotic genome activation and chromatin accessibility in the early Drosophila embryo [ChIP-seq]
Organism Drosophila melanogaster
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Following fertilization, the genomes of the germ cells are reprogrammed to form the totipotent embryo. Pioneer transcription factors are essential for remodeling the chromatin and driving the initial wave of zygotic gene expression. In Drosophila melanogaster, the pioneer factor Zelda is essential for development through this dramatic period of reprogramming, known as the maternal-to-zygotic transition (MZT). However, it was unknown whether additional pioneer factors were required for this transition. We identified an additional maternally encoded factor required for development through the MZT, GAGA Factor (GAF). GAF is necessary to activate widespread zygotic transcription and to remodel the chromatin accessibility landscape. We demonstrated that Zelda preferentially controls expression of the earliest transcribed genes, while genes expressed during widespread activation are predominantly dependent on GAF. Thus, progression through the MZT requires coordination of multiple pioneer-like factors, and we propose that as development proceeds control is gradually transferred from Zelda to GAF.
 
Overall design GAF ChIP-seq was performed in duplicate using anti-GFP antibody (Abcam #ab290) on embryos in which endogenous GAF protein was tagged with super folder GFP (sfGFP). Sequencing was performed on immunoprecipitated samles as well as input controls. Additional immunoprecipitations were performed using the anti-GFP antibody in w1118 to control for nonspecific pulldown. Zelda ChIP was performed in duplicate with the anti-Zelda antibody (Harrison et al., PLoS Genetics 2011) with input controls.
 
Contributor(s) Gaskill MM, Gibson TJ, Larson ED, Harrison MM
Citation(s) 33720012
Submission date Jun 18, 2020
Last update date May 06, 2021
Contact name Melissa M Harrison
E-mail(s) mharrison3@wisc.edu
Organization name University of Wisconsin Madison
Department Biomolecular Chemistry
Lab 1135 Biochemical Sciences Bldg
Street address 420 Henry Mall
City Madison
State/province WI
ZIP/Postal code 53706
Country USA
 
Platforms (1)
GPL21306 Illumina HiSeq 4000 (Drosophila melanogaster)
Samples (32)
GSM4626040 stage 3 GAF-sfGFP(C) GFP input replicate 1
GSM4626041 stage 3 GAF-sfGFP(C) GFP IP replicate 1
GSM4626042 stage 3 GAF-sfGFP(C) GFP input replicate 2
This SubSeries is part of SuperSeries:
GSE152773 GAF is essential for zygotic genome activation and chromatin accessibility in the early Drosophila embryo
Relations
BioProject PRJNA640381
SRA SRP267859

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
GSE152770_St3_GFPGAFC_antiGFP_IP_peaks.bed.gz 39.2 Kb (ftp)(http) BED
GSE152770_St3_GFPGAFC_antiGFP_IP_zscore.bw 57.6 Mb (ftp)(http) BW
GSE152770_St3_GFPGAFC_antiGFP_input_zscore.bw 63.6 Mb (ftp)(http) BW
GSE152770_St3_w1118_antiGFP_IP_zscore.bw 58.6 Mb (ftp)(http) BW
GSE152770_St3_w1118_antiGFP_input_zscore.bw 63.0 Mb (ftp)(http) BW
GSE152770_St5_GFPGAFC_antiGFP_IP_peaks.bed.gz 48.5 Kb (ftp)(http) BED
GSE152770_St5_GFPGAFC_antiGFP_IP_zscore.bw 64.8 Mb (ftp)(http) BW
GSE152770_St5_GFPGAFC_antiGFP_input_zscore.bw 65.7 Mb (ftp)(http) BW
GSE152770_St5_GFPGAFN_antiZLD_IP_zscore.bw 60.2 Mb (ftp)(http) BW
GSE152770_St5_GFPGAFN_control_antiGFP_IP_zscore.bw 56.5 Mb (ftp)(http) BW
GSE152770_St5_GFPGAFN_control_antiGFP_input_zscore.bw 60.5 Mb (ftp)(http) BW
GSE152770_St5_GFPGAFN_zld-RNAi_antiGFP_IP_zscore.bw 53.7 Mb (ftp)(http) BW
GSE152770_St5_w1118_antiGFP_IP_zscore.bw 64.1 Mb (ftp)(http) BW
GSE152770_St5_w1118_antiGFP_input_zscore.bw 66.7 Mb (ftp)(http) BW
GSE152770_st5_GAFdegradFP_antiZLD_IP_zscore.bw 58.1 Mb (ftp)(http) BW
GSE152770_st5_GAFdegradFP_antiZLD_input_zscore.bw 59.6 Mb (ftp)(http) BW
GSE152770_st5_GFPGAFN_antiZLD_IP_peaks.bed.gz 147.7 Kb (ftp)(http) BED
GSE152770_st5_GFPGAFN_antiZLD_input_zscore.bw 62.1 Mb (ftp)(http) BW
GSE152770_st5_GFPGAFN_control_antiGFP_IP_peaks.bed.gz 73.2 Kb (ftp)(http) BED
GSE152770_st5_GFPGAFN_zld-RNAi_antiGFP_IP_peaks.bed.gz 34.2 Kb (ftp)(http) BED
GSE152770_st5_GFPGAFN_zld-RNAi_antiGFP_input_zscore.bw 60.9 Mb (ftp)(http) BW
GSE152770_st5_degradFP_antiZLD_IP_peaks.bed.gz 60.9 Kb (ftp)(http) BED
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