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Series GSE63282 Query DataSets for GSE63282
Status Public on Apr 01, 2015
Title ChIP-seq and RNA-seq analyses identify Wnt and Fgf signaling pathways as Prep1 targets in mouse embryonic stem cells
Organism Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Expression profiling by high throughput sequencing
Summary The Prep1 (Pknox1) homeodomain transcription factor is essential at multiple stages of embryo development. In the E11.5 embryo trunk, we previously estimated that Prep1 binds about 3,300 genomic sites at a highly specific decameric consensus sequence, mainly governing basal cellular functions. We now show that in embryonic stem (ES) cells Prep1 binding pattern only partly overlaps that of the embryo trunk, with about 2,000 novel sites, highlighting a change of targets between embryonic differentiated v. embryonic stem cells. RNA-seq identifies about 1800 genes down-regulated in Prep1- /- ES cells which belong to gene ontology categories not enriched in the E11.5 Prep1i/i differentiated embryo, including in particular the Wnt and Fgf pathways. Indeed, we find aberrant Wnt and Fgf expression levels in the Prep1-/- ES cells which agrees with a deficient embryoid bodies (EBs) differentiation. Re-establishment of the Prep1 level rescues the phenotype.
Overall design [ChIP-Seq] Examination of genome-wide Prep1 binding in mouse ES cells using ChIP-seq and Illumina GAII sequencing.
[RNA-Seq] Examination of gene expression in wild type and Prep1-/- mouse ES cells using RNA-seq and Illumina GAII sequencing.
Contributor(s) Laurent A, Calabrese M, Warnatz HJ, Yaspo ML, Vsevolod V, Torres M, Blasi F, Penkov D
Citation(s) 25875616
Submission date Nov 14, 2014
Last update date May 15, 2019
Contact name Hans-Jörg Warnatz
Organization name Max Planck Institute for Molecular Genetics
Department Vertebrate Genomics
Lab Gene Expression and Regulation
Street address Ihnestrasse 63-73
City Berlin
ZIP/Postal code 14195
Country Germany
Platforms (1)
GPL9250 Illumina Genome Analyzer II (Mus musculus)
Samples (4)
GSM1545025 Prep1 (ChIP-Seq)
GSM1545026 Input_DNA (ChIP-Seq control)
GSM1545027 Mouse.ES.wild_type (RNA-Seq)
BioProject PRJNA267191
SRA SRP049804

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Supplementary file Size Download File type/resource
GSE63282_RAW.tar 1.5 Mb (http)(custom) TAR (of BED, RPKM)
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Raw data are available in SRA
Processed data provided as supplementary file

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