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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Apr 24, 2024 |
| Title |
Gene expression profiling of mouse embryonic stem cells with single-cell RNA sequencing |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Differences in gene-expression profiles between individual cells can give rise to distinct cell fate decisions. Yet how localisation on a micropattern impacts initial changes in mRNA, protein, and phosphoprotein abundance remains unclear. To identify the effect of cellular position on gene expression, we developed a scalable antibody and mRNA targeting sequential fluorescence in situ hybridization (ARTseq-FISH) method capable of simultaneously profiling mRNAs, proteins, and phosphoproteins in single cells. We studied 67 (phospho-)protein and mRNA targets in individual mouse embryonic stem cells (mESCs) cultured on circular micropatterns. To validate the detection of the mRNA targets quantified with ARTseq-FISH, we utilized single-cell RNA sequencing to profile a comparable population of mouse embryonic stem cells.
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| Overall design |
Mouse embryonic stem cells (mESCs) were seeded and growth in serum/LIF conditions. 30 hours post-seeding, cells were detached from the culture surface and frozen in preparation for single-cell RNA sequencing. Single-cell RNA sequencing was performed from a freshly thawed sample, through single-cell barcoding (10x Genomics Chromium) and sequencing (NextSeq 2000; Single Cell 3'v3 chemistry).
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| Contributor(s) |
García-Blay Ó, Hansen M |
| Citation(s) |
38724524 |
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| Submission date |
Apr 18, 2024 |
| Last update date |
Jun 27, 2024 |
| Contact name |
Oscar Garcia-Blay |
| E-mail(s) |
Oscar.GarciaBlay@ru.nl
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| Organization name |
Institute for Molecules and Materials (Radboud University)
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| Department |
Biophysical Chemistry
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| Lab |
Hansen Lab
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| Street address |
Heyendaalseweg 135
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| City |
Nijmegen |
| State/province |
Gelderland |
| ZIP/Postal code |
6525 AJ |
| Country |
Netherlands |
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| Platforms (1) |
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| Samples (1) |
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| Relations |
| BioProject |
PRJNA1102010 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE264348_RAW.tar |
103.2 Mb |
(http)(custom) |
TAR (of MTX, TSV) |
SRA Run Selector |
| Raw data are available in SRA |
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