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Mus musculus
25 Downloadable Samples
IlluminaHiSeq2000
Description
In contrast to urodele amphibians and teleost fish, mammals lack the regenerative responses to replace large body parts. Amphibian and fish regeneration uses dedifferentiation, i.e. reversal of differentiated state, as a means to produce progenitor cells to eventually replace damaged tissues. Therefore, activation of dedifferentiation response in mammalian tissues holds an immense promise for human regenerative medicine. msx2 expression has been shown to peak at the early time points of amphibian limb regeneration. Despite this temporal importance in the heterogenous regenerating limb tissues, the potential role of msx2 in dedifferentiation was previously not addressed in salamander or mammalian muscle cells. In order to test this, we ectopically overexpressed msx2 in mammalian myotubes and profiled their transcriptomes using next generation sequencing. We identified 4964 up-regulated and 4464 down-regulated transcripts in myotubes compared to myoblasts (uninduced GFP control cells; = 1.5 fold; FDR corrected p-values < 0.01). Upon ectopic msx2 expression in myotubes, 923 transcripts were downregulated, whereas 1283 transcripts were upregulated. Based on msx2's potential role in dedifferentiation, we reasoned that the transcripts, which are normally upregulated in myotubes in comparison to myoblasts, should go down upon msx2-expression. In accord with this idea, 575 myotube-enriched transcripts were downregulated after one day of ectopic msx2 expression. Similarly, 331 myoblast-enriched transcripts were upregulated upon msx2 expression. Overall design: To extensively analyze transcriptome-wide changes upon ectopic msx2 expression in mammalian myotubes, we performed next generation RNA-sequencing (RNA-seq) on uninduced and induced isolated myotubes that have msx2 and GFP or GFP alone transgenes. As a reference for the undifferentiated state, we also sequenced the transcriptomes of uninduced myoblast cultures of these two transgenic constructs. Deep sequencing was performed using Illumina HiSeq.
Publication Title
Ectopic expression of Msx2 in mammalian myotubes recapitulates aspects of amphibian muscle dedifferentiation.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 2 Downloadable Samples
Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
This is an initial experiment which was performed in order to identify novel transcriptional targets of the tumor suppressor p53
Publication Title
p53 activates the PANK1/miRNA-107 gene leading to downregulation of CDK6 and p130 cell cycle proteins.
Sample Metadata Fields
Specimen part, Cell line, Treatment
View Samples
GSE101973- Homo sapiens
- 6 Downloadable Samples
- Illumina HumanHT-12 V4.0 expression beadchip
Description
expression profiles kPSCs versus cMSC
Publication Title
The human kidney capsule contains a functionally distinct mesenchymal stromal cell population.
Sample Metadata Fields
Specimen part
View Samples- Pseudomonas aeruginosa
- 9 Downloadable Samples
- Affymetrix Pseudomonas aeruginosa Array (paeg1a)
Description
Pseudomonas aeruginosa is a common bacterium in the terminal plumbing system of buildings and it is from this niche that a substantial fraction of infections are acquired. To better understand P. aeruginosa biology in this environment, we examined the transcriptomes in tap water and pond water.
Publication Title
Transcriptional Responses of Pseudomonas aeruginosa to Potable Water and Freshwater.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 4 Downloadable Samples
- Affymetrix Human Genome U219 Array (hgu219)
Description
We found that LSD1 inhibition by a monoamine oxidase inhibitor, tranylcypromine (TC), could enhance fetal gamma globin expression.
Publication Title
Lysine-specific demethylase 1 is a therapeutic target for fetal hemoglobin induction.
Sample Metadata Fields
Treatment
View Samples GSE48832- Escherichia coli, Escherichia coli str. k-12 substr. mg1655
- 4 Downloadable Samples
- Affymetrix E. coli Genome 2.0 Array (ecoli2)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
COLOMBOS v2.0: an ever expanding collection of bacterial expression compendia.
Sample Metadata Fields
No sample metadata fields
View Samples- Escherichia coli
- 4 Downloadable Samples
- Affymetrix E. coli Genome 2.0 Array (ecoli2)
Description
Gene expression from Escherichia coli.
Publication Title
COLOMBOS v2.0: an ever expanding collection of bacterial expression compendia.
Sample Metadata Fields
No sample metadata fields
View Samples- Escherichia coli
- 20 Downloadable Samples
- Affymetrix E. coli Genome 2.0 Array (ecoli2)
Description
Having found that LexA degradation was significantly higher under apoptotic like death (ALD) than under SOS conditions, we hypothesized that additional genes tightly regulated by LexA would be transcribed under ALD conditions.
Publication Title
Apoptosis-like death, an extreme SOS response in Escherichia coli.
Sample Metadata Fields
Disease, Treatment
View Samples- Mus musculus
- 18 Downloadable Samples
- Affymetrix Mouse Gene 1.0 ST Array (mogene10st)
Description
DNA microarray analysis was performed with mouse multipotent adult germline stem cells (maGSCs) and embryonic stem cells (ESCs) from different genetic backgrounds cultured under standard ESC culture conditions and under differentiation-promoting conditions by the withdrawal of Leukemia Inhibitory Factor (LIF) and treatment with Retinoic Acid (RA). The analyzed undifferentiated cell lines are very similar based on their global gene expression pattern and show 97-99% identity dependent on the analyzed background. Only 621 genes are differentially expressed in cells derived from mouse 129SV-background, and 72 genes show differences in expression in cells generated from transgenic Stra8-EGFP/Rosa26-LacZ-background. Both maGSCs and ESCs express the same genes involved in the regulation of pluripotency, and even show no differences in the expression level of these genes. When comparing maGSCs with previously published signature genes of other pluripotent cell lines we could find that maGSCs share a very similar gene expression pattern with embryonic germ cells (EGCs). Also after differentiation of maGSCs and ESCs the transcriptomes of the cell lines are nearly identical which suggests that both cell types differentiate spontaneously in a very similar way. This is the first study comparing ESCs and a pluripotent cell line derived from an adult organism (maGSCs) on transcriptome level.
Publication Title
Pluripotent embryonic stem cells and multipotent adult germline stem cells reveal similar transcriptomes including pluripotency-related genes.
Sample Metadata Fields
Specimen part
View Samples- Homo sapiens
- 8 Downloadable Samples
- IlluminaGenomeAnalyzerIIx
Description
We profiled the dynamic, comprehensive transcriptome during human erythroid differentiation in vitro. The erythroid cells at day 4, 8, 11 and 14 differentiation stages were harvested and sequenced by Illumia 72 bp paired-end sequencing format, respectively. Overall design: Expression profiling of erythroid cells on differentiation days 4, 8, 11 and 14 and performed mRNA-seq on two biological replicates at each stage.
Publication Title
Modeling dynamic functional relationship networks and application to ex vivo human erythroid differentiation.
Sample Metadata Fields
No sample metadata fields
View Samples