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Series GSE104459 Query DataSets for GSE104459
Status Public on Feb 14, 2018
Title PITX1 Promotes Chondrogenesis and Myogenesis in Mouse Hindlimbs Through Conserved Regulatory Targets [RNA-Seq]
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary The PITX1 transcription factor is expressed during hindlimb development, where it plays a critical role in directing hindlimb growth and the specification of hindlimb morphology. While it is known that PITX1 regulates hindlimb formation, in part, through activation of the Tbx4 gene, other transcriptional targets remain to be elucidated. We have used a combination of ChIP-seq and RNA-seq to investigate enhancer regions and target genes that are directly regulated by PITX1 in embryonic mouse hindlimbs. In addition, we have analyzed PITX1 binding sites in hindlimbs of Anolis lizards to identify ancient PITX1 regulatory targets. We find that PITX1-bound regions in both mouse and Anolis hindlimbs are strongly associated with genes implicated in limb and skeletal system development. Gene expression analyses reveal a large number of misexpressed genes in the hindlimbs of Pitx1-/- embryos. By intersecting misexpressed genes with genes that have neighboring mouse PITX1 binding sites, we identified 440 candidate targets of PITX1. Of these candidates, 68 exhibit ultra-conserved PITX1 binding events that are shared between mouse and Anolis hindlimbs. Among the ancient targets of PITX1 are important regulators of cartilage and skeletal muscle development, including Sox9 and Six1. Our data suggest that PITX1 promotes chondrogenesis and myogenesis in the hindlimb by direct regulation of several key members of the cartilage and muscle transcriptional networks.
 
Overall design Hindlimb mRNA profiles of E9.5, E11.5 and E12.5 wild type (WT) and Pitx1-/- mice were generated by deep sequencing in triplicate.
 
Contributor(s) Wang JS, Infante CR, Park S, Menke DB
Citation(s) 29273440
Submission date Sep 29, 2017
Last update date May 15, 2019
Contact name Marc Wein
E-mail(s) mnwein@mgh.harvard.edu
Organization name Massachusetts General Hospital
Street address 55 Fruit Street
City Boston
State/province MA
ZIP/Postal code 02114
Country USA
 
Platforms (1)
GPL19057 Illumina NextSeq 500 (Mus musculus)
Samples (18)
GSM2800772 E9.5 WT Rep1
GSM2800773 E9.5 WT Rep2
GSM2800774 E9.5 WT Rep3
This SubSeries is part of SuperSeries:
GSE104460 PITX1 Promotes Chondrogenesis and Myogenesis in Mouse Hindlimbs Through Conserved Regulatory Targets
Relations
BioProject PRJNA412667
SRA SRP119167

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
GSE104459_PITX1_E11_5_HL_Gene_RPKM_Tracking.txt.gz 1.6 Mb (ftp)(http) TXT
GSE104459_PITX1_E12_5_HL_Gene_RPKM_Tracking.txt.gz 1.6 Mb (ftp)(http) TXT
GSE104459_PITX1_E9_5_HL_Gene_RPKM_Tracking.txt.gz 1.5 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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