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Series GSE151467 Query DataSets for GSE151467
Status Public on Jul 30, 2021
Title cis-regulation of Grem1 expression during limb development [ATAC HH24]
Organism Gallus gallus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Spatiotemporal gene expression programs are orchestrated by transcriptional enhancers which interact with target-gene promoters to regulate gene expression. The BMP antagonist Gremlin1 (Grem1) is an important node in the gene regulatory network that controls vertebrate limb development. In this study, we used a combination of open chromatin profiling (ATAC-seq) and chromatin immunoprecipitation sequencing (ChIP-seq) in mouse and chick to identify putative cis-regulatory modules (CRMs) that regulate Grem1 in limb buds. Using CRISPR/Cas genome editing we generated different Grem1 regulatory alleles lacking either individual CRMs, combinations or entire enhancer clusters. To study potential interactions of these CRMs with the Grem1 promoter, we generated 4C-seq profiles of specific regulatory alleles. Taken together our results revealed that the spatio-temporal changes in Grem1 expression are caused by cis-regulatory alterations due to the deletions of enhancer clusters rather than global changes in chromatin architecture.
 
Overall design ATAC-seq analysis on dissected HH24 chick wing buds
 
Contributor(s) Lopez-Rios J, Zeller R, Zuniga A, Geier F
Citation(s) 34548488
Submission date May 29, 2020
Last update date Nov 18, 2021
Contact name DBM Bioinformatics Core Facility
Phone +41612073541
Organization name University of Basel
Department Departement of Biomedicine
Street address Hebelstrasse 20
City Basel
State/province BS
ZIP/Postal code 4053
Country Switzerland
 
Platforms (1)
GPL19787 Illumina NextSeq 500 (Gallus gallus)
Samples (2)
GSM4579056 ATAC HH24 replicate 1
GSM4579057 ATAC HH24 replicate 2
This SubSeries is part of SuperSeries:
GSE151488 cis-regulation of Grem1 expression during limb development
Relations
BioProject PRJNA635921
SRA SRP265292

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
GSE151467_RAW.tar 296.4 Mb (http)(custom) TAR (of BIGWIG)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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