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| Status |
Public on Feb 03, 2017 |
| Title |
Vitamin C and L-Proline antagonistic effects capture alternative states in the pluripotency continuum [RNA-Seq] |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Samples 1-4 report RNA-seq transcriptome profiling of the L-Proline- (L-Pro) and bFgf/ActivinA- (F/A) derived mCherry+/eGFP+ (yellow) ESC population, using the Illumina HiSeq platform. Whole-genome expression revealed that more than 1000 genes were significantly deregulated in L-Pro- and F/A-induced cells compared to control (mCherry+/eGFP− red cells) and the two population shared up to 75% of deregulated genes with the same deregulation trend. Specifically, the pluripotency-associated genes were downregulated either at similar level (Nanog, Klf2, Klf4 and Gbx2) or at lower levels (up to 10 times) (Dppa 2, 3, 4, 5a, Rex1, Esrrb) in F/A- compared to L-Pro-treated cells. Interestingly, mesendodermal-related genes (e.g. Brachyury, Cer1, Dkk1, Eomes, Foxa2, and Sox17) were induced in both conditions but at significant higher levels in F/A- compared to L-Pro-treated cells. The transcriptome analysis of mCherry+/eGFP+ (yellow) cells supported the idea that L-Pro mimics F/A in inducing a naïve to primed transition, and suggested that it exerted a milder (weaker) effect. Samples 5-14 report RNA-seq transcriptome profiling of the mir-290_mCherry/mir-302_eGFP dual reporter ESCs (DRESCs) bulk culture, grown in FBS/LIF ± VitaminC (VitC) and L-Proline (L-Pro) and compared them to the standard naive/2i and primed/bFgf/ActivinA-EpiSCs (F/A), using the Illumina HiSeq platform. Whole-genome expression identified around 7900 deregulated genes in the different conditions, (fold change≥2 and pvalue<0.05). Principal component analysis (PCA) placed VitC between 2i and untreated control, and L-Pro between control and F/A. Accordingly, a set of pluripotency-associated genes was expressed at higher level in 2i and VitC conditions, while downregulated in L-Pro and F/A, compared to control. Conversely, priming markers were downregulated in 2i and VitC and upregulated in L-Pro and F/A compared to control The transcriptome analysis supported that VitC- and L-Pro captured alternative pluripotency states that can be likely placed between naïve/2i and primed/F/A states.
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| Overall design |
RNA-seq profiling of ESCs grown in FBS/LIF ± VitC, 2i, L-Pro or F/A, using the Illumina HiSeq platform
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| Contributor(s) |
Minchiotti G, D'Aniello C |
| Citation(s) |
28017658 |
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| Submission date |
Jul 07, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Cristina D'Aniello |
| E-mail(s) |
[email protected]
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| Organization name |
IGB-CNR
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| Street address |
Via Pietro Castellino, 111
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| City |
Naples |
| ZIP/Postal code |
80131 |
| Country |
Italy |
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| Platforms (2) |
| GPL17021 |
Illumina HiSeq 2500 (Mus musculus) |
| GPL19057 |
Illumina NextSeq 500 (Mus musculus) |
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| Samples (14)
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| This SubSeries is part of SuperSeries: |
| GSE84373 |
Vitamin C and L-Proline antagonistic effects capture alternative states in the pluripotency continuum |
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| Relations |
| BioProject |
PRJNA328130 |
| SRA |
SRP078054 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE84137_Combined_raw_count_table.txt.gz |
262.8 Kb |
(ftp)(http) |
TXT |
| GSE84137_Filtered_normalized_count_table.txt.gz |
162.9 Kb |
(ftp)(http) |
TXT |
| GSE84137_RAW.tar |
17.1 Mb |
(http)(custom) |
TAR (of TXT) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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