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Series GSE247510 Query DataSets for GSE247510
Status Public on Jul 18, 2024
Title Cadherins modulate the self-organizing potential of gastruloids (re-analysis)
Sample organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Third-party reanalysis
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.
 
Overall design reanalysis of single gastruloid RNA-seq
this is a reanalysis of some datasets from GSE106227 sample reanalysed are: GSM2832454, GSM2832455, GSM2832456, GSM2832457, GSM2832458, GSM2832459, GSM2832460, GSM2832461, GSM2832462, GSM2832463

Single-reads fastqs were retrieved from the SRA server using fasterq-dump version 3.0.5. They were trimmed for bad quality and Truseq adapters with Cutadapt v4.0 (-a CTGTCTCTTATACACATCTCCGAGCCCACGAGAC -q 30 -m 15). Mapping and counting were performed on filtered reads on the mouse genome mm10 with STAR version 2.7.8a44 with a custom gtf based on Ensembl version 10245 and ENCODE parameters. FPKM values were obtained by Cufflinks version 2.2.146,47 with options --no-effective-length-correction -b 'mm10.fa' --multiread-correct --library-type fr-firststrand --mask-file 'chrM_mm10.gtf' --max-bundle-length 10000000 --max-bundle-frags 1000000 (where chrM_mm10.gtf contains a transcript on each strand of the whole chrM). Uniquely mapped reads were filtered with bamFilter48 version 2.5.1. Coverages were computed with BEDTools49 version 2.30.0 for each strand using the '-scale' parameter to normalize to million uniquely mapped reads.
All the code required to reproduce the analysis is available here (https://github.com/MayranA/allScriptsFromMayranEtAl2023)

Processed data:
.bw: normalized coverage (to million of uniquely mapped reads) with both strands combined
AllCufflinks_Simplified.txt.gz: single table with all FPKM values from cufflinks
AllHTSeqCounts.txt.gz: single table with all counts from STAR

 
Contributor(s) Mayran 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 18, 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
 
This SubSeries is part of SuperSeries:
GSE247511 Cadherins modulate the self-organizing potential of gastruloids
Relations
Reanalysis of GSM2832454
Reanalysis of GSM2832455
Reanalysis of GSM2832456
Reanalysis of GSM2832457
Reanalysis of GSM2832458
Reanalysis of GSM2832459
Reanalysis of GSM2832460
Reanalysis of GSM2832461
Reanalysis of GSM2832462
Reanalysis of GSM2832463
BioProject PRJNA1039259

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
GSE247510_AllCufflinks_Simplified.txt.gz 1.8 Mb (ftp)(http) TXT
GSE247510_AllHTSeqCounts.txt.gz 526.8 Kb (ftp)(http) TXT
GSE247510_SRR6224362_both_strands.bw 85.8 Mb (ftp)(http) BW
GSE247510_SRR6224363_both_strands.bw 86.0 Mb (ftp)(http) BW
GSE247510_SRR6224364_both_strands.bw 84.1 Mb (ftp)(http) BW
GSE247510_SRR6224365_both_strands.bw 85.5 Mb (ftp)(http) BW
GSE247510_SRR6224366_both_strands.bw 82.6 Mb (ftp)(http) BW
GSE247510_SRR6224367_both_strands.bw 82.0 Mb (ftp)(http) BW
GSE247510_SRR6224368_both_strands.bw 83.4 Mb (ftp)(http) BW
GSE247510_SRR6224369_both_strands.bw 85.3 Mb (ftp)(http) BW
GSE247510_SRR6224370_both_strands.bw 76.2 Mb (ftp)(http) BW
GSE247510_SRR6224371_both_strands.bw 83.4 Mb (ftp)(http) BW
Raw data are available in SRA

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