|
| Status |
Public on Jul 18, 2024 |
| Title |
Cadherins modulate the self-organizing potential of gastruloids (RNA-seq) |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
Gastruloids have recently emerged as an efficient four-dimensional model for studying some aspects of post-implantation embryonic patterning. Their ability to undergo gastrulation-like processes leading to the self-organization into highly reproducible biological objects, has opened new avenues to investigate early embryonic patterning. Here, we sought to uncover the molecular and cellular mechanism underlying this remarkable property. We report that self-organization competence is associated with a cell-specific coordination of a Cadherin switch. We find that N-Cadherin hinders gastruloids morphogenetic competence, for its inactivation leads to the formation of trunk-like structures without relying on the otherwise requested extra-cellular matrix analogues such as Matrigel. In contrast, the repression of E-Cadherin by Snai1 is critical for self-organization: Snai1 establishes a cell-specific repressive pace by triggering the repression of a pluripotency-associated transcription program and its chromatin landscape, thus allowing a proper transition from E- to N-Cadherin to occur. Altogether, this work establishes a molecular mechanism that integrates the exit from pluripotency and the pace of cell differentiation, leading to the observed self-organizing potential of gastruloids.
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| |
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| Overall design |
Bulk RNA-seq on gastruloids from WT and mutant conditions
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| |
|
| Contributor(s) |
Mayran A, Cossy A, Lopez-Delisle L, Duboule D |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
| |
| Submission date |
Nov 11, 2023 |
| Last update date |
Jul 19, 2024 |
| Contact name |
ALEXANDRE MAYRAN |
| E-mail(s) |
alexandre.mayran@epfl.ch
|
| Organization name |
EPFL
|
| Street address |
Station 19
|
| City |
LAUSANNE |
| State/province |
Waadt |
| ZIP/Postal code |
1015 |
| Country |
Switzerland |
| |
|
| Platforms (1) |
| GPL24247 |
Illumina NovaSeq 6000 (Mus musculus) |
|
| Samples (39)
|
| GSM7890890 |
RNAseq of 48h WT gastruloids replicate1 |
| GSM7890891 |
RNAseq of 48h WT gastruloids replicate2 |
| GSM7890892 |
RNAseq of 48h WT gastruloids replicate3 |
| GSM7890893 |
RNAseq of 54h WT gastruloids replicate1 |
| GSM7890894 |
RNAseq of 54h WT gastruloids replicate2 |
| GSM7890895 |
RNAseq of 54h WT gastruloids replicate3 |
| GSM7890896 |
RNAseq of 60h WT gastruloids replicate1 |
| GSM7890897 |
RNAseq of 60h WT gastruloids replicate2 |
| GSM7890898 |
RNAseq of 60h WT gastruloids replicate3 |
| GSM7890899 |
RNAseq of 66h WT gastruloids replicate1 |
| GSM7890900 |
RNAseq of 66h WT gastruloids replicate2 |
| GSM7890901 |
RNAseq of 66h WT gastruloids replicate3 |
| GSM7890902 |
RNAseq of 72h WT gastruloids replicate1 |
| GSM7890903 |
RNAseq of 72h WT gastruloids replicate2 |
| GSM7890904 |
RNAseq of 72h WT gastruloids replicate3 |
| GSM7890905 |
RNAseq of 78h WT gastruloids replicate1 |
| GSM7890906 |
RNAseq of 78h WT gastruloids replicate2 |
| GSM7890907 |
RNAseq of 78h WT gastruloids replicate3 |
| GSM7890908 |
RNAseq of 84h WT gastruloids replicate1 |
| GSM7890909 |
RNAseq of 84h WT gastruloids replicate2 |
| GSM7890910 |
RNAseq of 84h WT gastruloids replicate3 |
| GSM7890911 |
RNAseq of 90h WT gastruloids replicate1 |
| GSM7890912 |
RNAseq of 90h WT gastruloids replicate2 |
| GSM7890913 |
RNAseq of 90h WT gastruloids replicate3 |
| GSM7890914 |
RNAseq of 96h WT gastruloids replicate1 |
| GSM7890915 |
RNAseq of 96h WT gastruloids replicate2 |
| GSM7890916 |
RNAseq of 96h WT gastruloids replicate3 |
| GSM7890917 |
RNAseq of 120h Cdh2 Het gastruloids replicate1 |
| GSM7890918 |
RNAseq of 120h Cdh2 Het gastruloids replicate2 |
| GSM7890919 |
RNAseq of 120h Cdh2 KO clone 1 gastruloids replicate1 |
| GSM7890920 |
RNAseq of 120h Cdh2 KO clone 1 gastruloids replicate2 |
| GSM7890921 |
RNAseq of 120h Cdh2 KO clone 2 gastruloids replicate1 |
| GSM7890922 |
RNAseq of 120h Cdh2 KO clone 2 gastruloids replicate2 |
| GSM7890923 |
RNAseq of 96h WT gastruloids replicate4 |
| GSM7890924 |
RNAseq of 96h WT gastruloids replicate5 |
| GSM7890925 |
RNAseq of 96h Snai1 KO clone 1 gastruloids replicate1 |
| GSM7890926 |
RNAseq of 96h Snai1 KO clone 1 gastruloids replicate2 |
| GSM7890927 |
RNAseq of 96h Snai1 KO clone 2 gastruloids replicate1 |
| GSM7890928 |
RNAseq of 96h Snai1 KO clone 2 gastruloids replicate2 |
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| This SubSeries is part of SuperSeries: |
| GSE247511 |
Cadherins modulate the self-organizing potential of gastruloids |
|
| Relations |
| BioProject |
PRJNA1039256 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE247508_120h_Cdh2Het_both_strands.bw |
118.0 Mb |
(ftp)(http) |
BW |
| GSE247508_120h_Cdh2Het_negative_strand.bw |
58.6 Mb |
(ftp)(http) |
BW |
| GSE247508_120h_Cdh2Het_positive_strand.bw |
60.0 Mb |
(ftp)(http) |
BW |
| GSE247508_120h_Cdh2KO_Clone1_both_strands.bw |
123.8 Mb |
(ftp)(http) |
BW |
| GSE247508_120h_Cdh2KO_Clone1_negative_strand.bw |
62.8 Mb |
(ftp)(http) |
BW |
| GSE247508_120h_Cdh2KO_Clone1_positive_strand.bw |
64.1 Mb |
(ftp)(http) |
BW |
| GSE247508_120h_Cdh2KO_Clone2_both_strands.bw |
113.8 Mb |
(ftp)(http) |
BW |
| GSE247508_120h_Cdh2KO_Clone2_negative_strand.bw |
56.8 Mb |
(ftp)(http) |
BW |
| GSE247508_120h_Cdh2KO_Clone2_positive_strand.bw |
58.0 Mb |
(ftp)(http) |
BW |
| GSE247508_48h_WT_both_strands.bw |
134.1 Mb |
(ftp)(http) |
BW |
| GSE247508_48h_WT_negative_strand.bw |
66.7 Mb |
(ftp)(http) |
BW |
| GSE247508_48h_WT_positive_strand.bw |
68.2 Mb |
(ftp)(http) |
BW |
| GSE247508_54h_WT_both_strands.bw |
137.2 Mb |
(ftp)(http) |
BW |
| GSE247508_54h_WT_negative_strand.bw |
68.6 Mb |
(ftp)(http) |
BW |
| GSE247508_54h_WT_positive_strand.bw |
69.8 Mb |
(ftp)(http) |
BW |
| GSE247508_60h_WT_both_strands.bw |
138.8 Mb |
(ftp)(http) |
BW |
| GSE247508_60h_WT_negative_strand.bw |
69.6 Mb |
(ftp)(http) |
BW |
| GSE247508_60h_WT_positive_strand.bw |
70.6 Mb |
(ftp)(http) |
BW |
| GSE247508_66h_WT_both_strands.bw |
133.5 Mb |
(ftp)(http) |
BW |
| GSE247508_66h_WT_negative_strand.bw |
66.5 Mb |
(ftp)(http) |
BW |
| GSE247508_66h_WT_positive_strand.bw |
68.0 Mb |
(ftp)(http) |
BW |
| GSE247508_72h_WT_both_strands.bw |
127.7 Mb |
(ftp)(http) |
BW |
| GSE247508_72h_WT_negative_strand.bw |
64.2 Mb |
(ftp)(http) |
BW |
| GSE247508_72h_WT_positive_strand.bw |
65.2 Mb |
(ftp)(http) |
BW |
| GSE247508_78h_WT_both_strands.bw |
142.1 Mb |
(ftp)(http) |
BW |
| GSE247508_78h_WT_negative_strand.bw |
71.0 Mb |
(ftp)(http) |
BW |
| GSE247508_78h_WT_positive_strand.bw |
71.8 Mb |
(ftp)(http) |
BW |
| GSE247508_84h_WT_both_strands.bw |
146.6 Mb |
(ftp)(http) |
BW |
| GSE247508_84h_WT_negative_strand.bw |
72.8 Mb |
(ftp)(http) |
BW |
| GSE247508_84h_WT_positive_strand.bw |
74.4 Mb |
(ftp)(http) |
BW |
| GSE247508_90h_WT_both_strands.bw |
140.3 Mb |
(ftp)(http) |
BW |
| GSE247508_90h_WT_negative_strand.bw |
70.1 Mb |
(ftp)(http) |
BW |
| GSE247508_90h_WT_positive_strand.bw |
71.3 Mb |
(ftp)(http) |
BW |
| GSE247508_96h_Snai1KO_Clone1_both_strands.bw |
140.3 Mb |
(ftp)(http) |
BW |
| GSE247508_96h_Snai1KO_Clone1_negative_strand.bw |
70.5 Mb |
(ftp)(http) |
BW |
| GSE247508_96h_Snai1KO_Clone1_positive_strand.bw |
71.7 Mb |
(ftp)(http) |
BW |
| GSE247508_96h_Snai1KO_Clone2_both_strands.bw |
132.4 Mb |
(ftp)(http) |
BW |
| GSE247508_96h_Snai1KO_Clone2_negative_strand.bw |
66.9 Mb |
(ftp)(http) |
BW |
| GSE247508_96h_Snai1KO_Clone2_positive_strand.bw |
68.3 Mb |
(ftp)(http) |
BW |
| GSE247508_96h_Snai1WT_both_strands.bw |
135.3 Mb |
(ftp)(http) |
BW |
| GSE247508_96h_Snai1WT_negative_strand.bw |
67.4 Mb |
(ftp)(http) |
BW |
| GSE247508_96h_Snai1WT_positive_strand.bw |
68.6 Mb |
(ftp)(http) |
BW |
| GSE247508_96h_WT_both_strands.bw |
146.0 Mb |
(ftp)(http) |
BW |
| GSE247508_96h_WT_negative_strand.bw |
72.8 Mb |
(ftp)(http) |
BW |
| GSE247508_96h_WT_positive_strand.bw |
74.1 Mb |
(ftp)(http) |
BW |
| GSE247508_DESeq2_summary.txt.gz |
1.2 Mb |
(ftp)(http) |
TXT |
| GSE247508_DESeq2_summary_long.txt.gz |
1.9 Mb |
(ftp)(http) |
TXT |
| GSE247508_RAW.tar |
8.8 Gb |
(http)(custom) |
TAR (of BW) |
| GSE247508_tables_mutants.tar.gz |
2.4 Mb |
(ftp)(http) |
TAR |
| GSE247508_tables_time_course.tar.gz |
3.9 Mb |
(ftp)(http) |
TAR |
SRA Run Selector |
| Raw data are available in SRA |
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