Filters
Technology
Platform
GSE42081
Mus musculus, Rattus norvegicus
12 Downloadable Samples
Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
The transition between morula and blastocyst stage during preimplantation development represents the first differentiation event of embryogenesis. Morula cells undergo the first cellular specialization and produce two well-defined populations of cells, the trophoblast and the inner cell mass (ICM). Embryonic stem cells (ESCs) with unlimited self-renewal capacity are believed to represent the in vitro counterpart of the ICM. Both mouse and rat ESCs can be derived from the ICM cells, but their in vitro stability differs. In this study we performed a microarray analysis in which we compared the transcriptome of mouse and rat morula, blastocyst, and ICM. This cross-species comparison represents a good model for understanding the differences in derivation and cultivation of ESCs observed in the two species. In order to identify alternative regulation of important molecular mechanisms the investigation of differential gene expression between the two species was extended at the level of signaling pathways, gene families, and single selected genes of interest. Some of the genes differentially expressed between the two species are already known to be important factors in the maintenance of pluripotency in ESCs, like for example Sox2 or Stat3, or play a role in reprogramming somatic cells to pluripotency like c-Myc, Klf4 and p53 and therefore represent interesting candidates to further analyze in vitro in the rat ESCs. This is the first study investigating the gene expression changes during the transition from morula to blastocyst in the rat preimplantation development. Our data show that in the pluripotent pool of cells of the rat and mouse preimplantation embryo substantial differential regulation of genes is present, which might explain the difficulties observed for the derivation and culture of rat ESCs using mouse conditions
Publication Title
Cross-species genome wide expression analysis during pluripotent cell determination in mouse and rat preimplantation embryos.
Sample Metadata Fields
Sex, Age, Specimen part
View Samples- Mus musculus
- 35 Downloadable Samples
Illumina HiSeq 2500
Description
Our study looks at the dirsruption of lung circadian transcriptome that occurs when neutrophils are depleted (by application of antibodies (anti-Ly6G-1A8) to wildtype C57BL/6 mice, or Diphtheria toxin (DT) to neutrophil-specific DT-susceptible mice (MRP8-Cre;iDTR-flox)). Overall design: Lungs were harvested from neutrophil-depleted (antibody or DT) or non-depleted mice, in normal light-controlled mouse facility (ZT4) or 12h inverted light cabinets (ZT16). Experiments were carried out over 3 batches (July 2017, September 2017, and April 2018), with 3 or 4 mice per group. Antibody-depleted and non-depleted mice were tested for the July 2017 and September 2017 batches, whereas DT-depleted mice were tested only in April 2018.
Publication Title
Neutrophils instruct homeostatic and pathological states in naive tissues.
Sample Metadata Fields
Specimen part, Treatment, Subject
View Samples- Mus musculus
- 4 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
IKKbeta is a subunit of the IkB kinase (IKK) complex required for NF-kB activation in response to pro-inflammatory signals. NF-kB regulates the expression of many genes involved in inflammation, immunity and apoptosis, and also controls cell proliferation and differentiation in different tissues; however, its function in skin physiopathology remains controversial. We here report the alterations caused by increased IKKbeta activity in basal cells of the skin of transgenic mice.
Publication Title
IKKbeta leads to an inflammatory skin disease resembling interface dermatitis.
Sample Metadata Fields
Sex, Age, Specimen part
View Samples- Mus musculus
- 35 Downloadable Samples
- NextSeq 500
Description
Ultra low input sequencing of FACS sorted primary murine microglia from CSF-1 or IL-34 deficient forebrain and cerebella, at P8 and 9 weeks Overall design: Csf1fl/fl vs NesCreCsf1fl/fl: 3-4 biological replicates per timepoint per group; Il34wt/wt vs Il34Lacz/Lacz: 2-3 biological replicates per timepoint per group. P8, 9weeks
Publication Title
CSF-1 controls cerebellar microglia and is required for motor function and social interaction.
Sample Metadata Fields
Age, Specimen part, Subject
View Samples- Mus musculus
- 18 Downloadable Samples
- Affymetrix Murine Genome U74A Version 2 Array (mgu74av2)
Description
To investigate the importance of STAT3 in the establishment of ES cells we have in a first step derived stable pluripotent embryonic stem cells from transgenic FVB mice expressing a conditional tamoxifen dependent STAT3-MER fusion protein. In a second step, STAT3-MER overexpressing cells were used to identify STAT3 pathway-related genes by expression profiling in order to identify new key-players involved in maintenance of pluripotency in ES cells.
Publication Title
Expression profiling in transgenic FVB/N embryonic stem cells overexpressing STAT3.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 14 Downloadable Samples
- Illumina HiSeq 2500
Description
Our study aims to analyze time-dependent changes in neutrophil phenotype, compare them with included neutrophil-specific mutants, and indentify common signatures among the 5 groups Overall design: Blood neutrophils from wild-type and mutants were isolated based on Ly6G staining, then standard RNA extraction procedures were performed. Wild-type samples were extracted at ZT5 and ZT13, all other samples at ZT5.
Publication Title
A Neutrophil Timer Coordinates Immune Defense and Vascular Protection.
Sample Metadata Fields
Sex, Specimen part, Cell line, Subject
View Samples- Mus musculus
- 5 Downloadable Samples
- Illumina HiSeq 2500
Description
Our study aims to analyze time-dependent changes in neutrophil phenotype Overall design: Blood neutrophils were isolated based on Ly6G staining, then standard RNA extraction procedures were performed. This samples were extracted at ZT13.
Publication Title
A Neutrophil Timer Coordinates Immune Defense and Vascular Protection.
Sample Metadata Fields
Specimen part, Subject
View Samples- Mus musculus
- 18 Downloadable Samples
- Affymetrix Mouse Gene 1.0 ST Array (mogene10st)
Description
Background and aims: The transcription factor Stat3 has been considered to promote progression and metastasis of intestinal cancers.
Publication Title
Stat3 is a negative regulator of intestinal tumor progression in Apc(Min) mice.
Sample Metadata Fields
Sex, Specimen part
View Samples- Homo sapiens
- 16 Downloadable Samples
- IlluminaHiSeq2500
Description
Familial Dysautonomia is a genetic disease, however patietns with the same genotype present with mild or severe forms of the disease. We used the pluripotent stem cell technology to capture the differences in disease severity in vitro during neurodevelopment as well as during maintanance of the cells, showing developmental and degenerative phenotypes. RNA seq. analysis of the groups confirmed those diffferences. Overall design: Analysis of RNA from PSC-derived neural crest cells from severe FD, mild FD and healthy patients
Publication Title
Capturing the biology of disease severity in a PSC-based model of familial dysautonomia.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 6 Downloadable Samples
- IlluminaHiSeq2000
Description
We have generated expression profiles of induced pluripotent stem cells (iPSCs) and iPSC-derived neural crest populations from Familial Dysautonomia patients. These profiles were compared to a normal iPSC line that does not harbor the IKBKAP mutation. Overall design: All cell types were differentiated from patient derived iPSCs. Bulk iPSCs were harvested for RNA and the neural crest populations were sorted on day 18 for p75/HNK1 before RNA isolation.
Publication Title
Capturing the biology of disease severity in a PSC-based model of familial dysautonomia.
Sample Metadata Fields
No sample metadata fields
View Samples