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Series GSE224905 Query DataSets for GSE224905
Status Public on Apr 28, 2023
Title Sequential and directional insulation by conserved CTCF sites underlies the Hox timer in stembryos [scRNA-seq]
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary During development, Hox genes are activated in a time sequence following their relative positions on their clusters, leading to the proper identities of structures along the rostral to caudal axis. To understand the mechanism operating this Hox timer, we used ES-cells derived stembryos and show that the core of the process involves the start of transcription at the anterior part of the cluster, following Wnt signaling, and a concomitant loading of cohesin complexes enriched on the transcribed DNA segments, i.e., with an asymmetric distribution in favor of the anterior part the gene cluster. Chromatin extrusion then occurs with, along with time, successively more posterior CTCF sites acting as transient insulators, thus generating a progressive time-delay in the activation of more posterior-located genes due to long-range contacts with a flanking TAD. Mutant stembryos support this model and reveal that the iterated presence of evolutionary conserved and regularly spaced intergenic CTCF sites control the precision and the pace of this temporal mechanism.
 
Overall design Single Cell RNA-seq data of stembryos
 
Contributor(s) Rekaik H, Lopez-Delisle L, Mascrez B, Bochaton C, Mayran A, Duboule D
Citation(s) 37322110
Submission date Feb 09, 2023
Last update date Aug 08, 2023
Contact name Lucille Lopez-Delisle
E-mail(s) lucille.delisle@epfl.ch
Organization name EPFL
Street address Station 19
City Lausanne
ZIP/Postal code 1015
Country Switzerland
 
Platforms (2)
GPL19057 Illumina NextSeq 500 (Mus musculus)
GPL21103 Illumina HiSeq 4000 (Mus musculus)
Samples (6)
GSM7035394 scRNA-seq of the anterior part of wt stembryos at 120h, rep1
GSM7035395 scRNA-seq of the posterior part of wt stembryos at 120h, rep1
GSM7035396 scRNA-seq of the whole wt stembryos at 120h, rep1
This SubSeries is part of SuperSeries:
GSE205783 Sequential and directional insulation by conserved CTCF sites underlies the Hox timer in stembryos
Relations
BioProject PRJNA933096

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Supplementary file Size Download File type/resource
GSE224905_combined.96h.120h.rds.gz 1.0 Gb (ftp)(http) RDS
GSE224905_filtered_feature_bc_matrix.tar.gz 419.0 Mb (ftp)(http) TAR
GSE224905_metadata.csv.gz 1.2 Mb (ftp)(http) CSV
GSE224905_raw_counts.csv.gz 85.0 Mb (ftp)(http) CSV
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Raw data are available in SRA
Processed data are available on Series record

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