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Series GSE221159 Query DataSets for GSE221159
Status Public on Feb 24, 2024
Title Spatiotemporally resolved ex vivo colorectal cancer development in engineered mini-colons (RNA-Seq AKP lines)
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary Here we developed topobiologically complex mini-colons able to undergo tumorigenesis ex vivo by integrating microfabrication, optogenetic, and tissue engineering approaches. With this system, tumorigenic transformation can be spatiotemporally controlled by directing oncogenic activation through blue-light exposure, and emerging colon tumors can be tracked in real-time with single-cell resolution for several weeks without breaking the culture. These induced mini-colons display rich intra- and inter-tumoral diversity and recapitulate key pathophysiological hallmarks displayed by colorectal tumors in vivo. By fine-tuning cell-intrinsic and extrinsic parameters, mini-colons can be leveraged to unveil tumorigenic determinants, including dietary patterns, microbiota-derived metabolites, and pharmacological therapies.
 
Overall design Gene expression profiling analysis of bulk RNA-seq data from colon organoid lines derived from: healthy colon (control), OptoCre-induced AKP organoids (organoid AKP), OptoCre-induced AKP mini-colons (mini-colon AKP), in vivo colon tumors (in vivo AKP).
 
Contributor(s) Lorenzo-Martín LF, Hübscher T, Broguiere N, Bowler A, Langer J, Tillard L, Nikolaev M, Radtke F, Lutolf MP
Citation(s) 38658753
Submission date Dec 16, 2022
Last update date May 17, 2024
Contact name L. Francisco Lorenzo-Martín
E-mail(s) luis.lorenzomartin@epfl.ch
Organization name École Polytechnique Fédérale de Lausanne (EPFL)
Lab Laboratory of Stem Cell Bioengineering
Street address EPFL – SV – IBI – LSCB – Station 15
City Lausanne
State/province Vaud
ZIP/Postal code 1015
Country Switzerland
 
Platforms (1)
GPL19057 Illumina NextSeq 500 (Mus musculus)
Samples (33)
GSM6846556 Control rep1
GSM6846557 Control rep2
GSM6846558 Control rep3
This SubSeries is part of SuperSeries:
GSE221163 Spatiotemporally resolved ex vivo colorectal cancer development in engineered mini-colons
Relations
BioProject PRJNA913133

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
GSE221159_RAW.tar 4.4 Mb (http)(custom) TAR (of TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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