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Series GSE64055 Query DataSets for GSE64055
Status Public on Oct 01, 2015
Title Identifying active cis-regulatory elements during the development of the limbs and external genitalia in the mouse and lizard.
Organisms Mus musculus; Anolis carolinensis
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary The morphologies of the amniote phallus and limbs differ dramatically, but these structures share signaling pathways and patterns of gene expression in early development. Thus far, the extent to which genital and limb transcriptional networks share cis-regulatory elements has remained unexplored. Using chromatin immunoprecipitation with an antibody against the histone modification mark H3K27ac followed by Illumina high-throughput sequencing, we identify thousands of active enhancers in developing limbs, genital tubercle, and additional embryonic tissues of the mouse and green anole lizard (Anolis carolinensis). We show in global analyses of cis-regulatory activity that embryonic limbs and genitalia display overlapping patterns of enhancer activity, and that many H3K27ac-marked regions are shared between mouse and green anole. Our findings support the hypothesis that the amniote phallus evolved through co-option of a preexisting appendage developmental program.
 
Overall design ChIP-Seq was performed using an antibody against the histone mark H3K27ac on mouse E11.5 forelimb (2 replicates), E11.5 hindlimb (2 replicates), E12.5 genital tubercle (2 replicates), E11.5 flank mesenchyme (single sample), and E10.5 eye (2 replicates). For the green anole lizard, H3K27ac ChIP-Seq was performed on single replicates of pooled stage TS7/8 forelimbs, TS7/8 hindlimbs, or TS9 to TS11 hemiphallus. For each tissue type, a sample of sheared chromatin prior to antibody incubation and pulldown (input DNA) was saved for the generation of control libraries to detect enrichment in the ChIP samples.
 
Contributor(s) Infante CR, Mihala AG, Park S, Lauderdale JD, Menke DB
Citation(s) 26439399
Submission date Dec 10, 2014
Last update date May 15, 2019
Contact name Carlos Rafael Infante
E-mail(s) cinfante@uga.edu
Organization name University of Georgia
Department Genetics
Lab Menke
Street address 500 D.W. Brooks Dr
City Athens
State/province GA
ZIP/Postal code 30602
Country USA
 
Platforms (2)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
GPL15001 Illumina HiSeq 2000 (Anolis carolinensis)
Samples (21)
GSM1563530 Forelimb_H3K27ac_Replicate1
GSM1563531 Forelimb_H3K27ac_Replicate2
GSM1563532 Forelimb_Input_DNA
Relations
BioProject PRJNA269973
SRA SRP051043

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Supplementary file Size Download File type/resource
GSE64055_RAW.tar 8.7 Gb (http)(custom) TAR (of BED, BW)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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