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Series GSE71990 Query DataSets for GSE71990
Status Public on Jul 27, 2016
Title Identification of genome wide targets of the hox protein Ultrabithorax (Ubx) in larval wing buds of Bombyx mori (Daizo)
Organism Bombyx mori
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Amongst the various different insect groups, there is remarkable diversity in the number and size of wings. However the development of the basic body plan in insects is similar to a large extent. The genes of the hox complex regulate various pathways to bring about the development or modification of different organs. Ubx, a gene of the bithorax hox complex is expressed in the third thoracic segment of insects and is known to specify the fate of wing appendage in that segment.To understand the role of Ubx and how its regulatory mechanism has evolved through the course of evolution we have compared its genome wide targets in different insect orders. The identification of regulatory pathways and the key players Ubx regulates is crucial to understand how it has controlled wing development across insect orders. Our lab has previously identified direct targets of Ubx in Drosophila using ChIP-chip (Agrawal et al, 2011). To further our knowledge on the role of regulation in development and modification of hind wing appendage we have studied the targets in the hind wings of other insects (silk moth; Lepidoptera and honeybee; Hymenoptera) and performed a comparative analysis. We have employed ChIP followed by illumina sequencing to identify the targets of Ubx in developing hind and fore wing buds of Bombyx larvae. This is a first next generation sequencing study in Lepidoptera in an attempt to understand wing development.
 
Overall design Chromatin Immunoprecipitation (ChIP) was used to identify genome wide targets bound by Ubx in Bombyx larval wing buds. The experiment to enrich Ubx bound regions was carried out using a Bombyx N terminal-Ubx specific poylclonal antibody raised in Rabbit and purified against a Protein A column to obtain IgG fraction. An Immunoprecipitation (IP) with Normal Rabbit IgG was used as a negative control to eliminate the regions that pertained to non specific binding to an Immunogloubulin. The normalization of both ChIP and IgG was done against sequenced input chromatin. Two replicates of single end 36 bp reads were sequenced using Ilumina for all the three conditions and for both fore and hind wing tissue samples.The peaks common to both the replicates were considered after applying a FDR cutoff.The fore wing target set was used for comparison with the hind wing targets.
 
Contributor(s) Tarikere S, Shashidhara LS
Citation(s) 27296678
Submission date Aug 12, 2015
Last update date May 15, 2019
Contact name Shreeharsha Tarikere
E-mail(s) harsha.tts@gmail.com
Organization name Harvard University
Department Organismic and Evolutionary Biology
Lab Dr.Cassandra G. Extavour
Street address 16 Divinity Avenue, Biolabs
City Cambridge
State/province Massachusetts
ZIP/Postal code 02138
Country USA
 
Platforms (1)
GPL9151 Illumina Genome Analyzer II (Bombyx mori)
Samples (12)
GSM1849357 Hind wing anti Ubx ChIP pulldown rep1
GSM1849358 Hind wing Input chromatin rep1
GSM1849359 Hind wing negative IgG control rep1
This SubSeries is part of SuperSeries:
GSE71992 A comparative genomic analysis of targets of Hox protein Ultrabithorax amongst distant insect species.
Relations
BioProject PRJNA292691
SRA SRP062330

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Supplementary file Size Download File type/resource
GSE71990_Fore_wing_peaks_common_between_replicates1_2.bed.gz 7.0 Kb (ftp)(http) BED
GSE71990_Hind_wing_peaks_common_between_replicates1_2.bed.gz 22.6 Kb (ftp)(http) BED
GSE71990_RAW.tar 3.1 Mb (http)(custom) TAR (of XLS)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record
Processed data provided as supplementary file

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