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SRP107747
Homo sapiens
18 Downloadable Samples
Illumina HiSeq 2000
Description
Organoid technology provides the possibility to culture human colon tissue and patient-derived colorectal cancers (CRC) while maintaining all functional and phenotypic characteristics. Labeling of human colon stem cells (CoSCs), especially in normal and benign tumor organoids, is challenging and therefore limits usability of multi-patient organoid libraries for CoSC research. Here, we developed STAR (STem cell Ascl2 Reporter), a minimal enhancer/promoter element that reports transcriptional activity of ASCL2, a master regulator of LGR5+ CoSC fate. Among others via lentiviral infection, STAR minigene labels stem cells in normal as well as in multiple engineered and patient-derived CRC organoids of different stage and genetic make-up. STAR revealed that stem cell driven differentiation hierarchies and the capacity of cell fate plasticity (de-differentiation) are present at all stages of human CRC development. The flexible and user-friendly nature of STAR applications in combination with organoid technology will facilitate basic research on human adult stem cell biology. Overall design: Cells from different colon organoid types were FACS sorted for stem STemness Ascl2 Reporter activity for transcriptome profiling by RNA-seq.
Publication Title
Specific Labeling of Stem Cell Activity in Human Colorectal Organoids Using an ASCL2-Responsive Minigene.
Sample Metadata Fields
Subject
View Samples- Mus musculus
- 4 Downloadable Samples
- NextSeq 500
Description
The Nucleosome Remodeling and Deacetylase (NuRD) complex plays an important role in gene expression regulation, stem cell self-renewal, and lineage commitment. Yet little is known about the dynamics of NuRD during cellular differentiation. Here, we study these dynamics using genome-wide profiling and quantitative interaction proteomics in mouse embryonic stem cells (ESCs) and neural progenitor cells (NPCs). The genomic targets of NuRD are highly dynamic during differentiation, with most binding occurring at cell-type specific promoters and enhancers. We identify ZFP296 as a novel, ESC-specific NuRD interactor that also interacts with the SIN3A complex. ChIP-sequencing in Zfp296 knockout (KO) ESCs reveals decreased NuRD binding both genome-wide and at ZFP296 binding sites, although this has little effect on the transcriptome. Nevertheless, Zfp296 KO ESCs exhibit delayed induction of lineage-specific markers upon differentiation to embryoid bodies. In summary, we identify an ESC-specific NuRD interacting protein which regulates genome-wide NuRD binding and cellular differentiation. Overall design: RNA-seq samples of wildtype R1 ESCs and Zfp296 CRISPR KO clone 2 R1 ESCs
Publication Title
NuRD-interacting protein ZFP296 regulates genome-wide NuRD localization and differentiation of mouse embryonic stem cells.
Sample Metadata Fields
Specimen part, Subject
View Samples- Mus musculus
- 4 Downloadable Samples
Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
The ETS1 transcription factor is required for the development and cytokine-induced expansion of ILC2
Publication Title
The ETS1 transcription factor is required for the development and cytokine-induced expansion of ILC2.
Sample Metadata Fields
Specimen part
View Samples- Mus musculus
- 46 Downloadable Samples
- Ion Torrent Proton
Description
For up to 70 weeks we subcutaneuously injected two hundered p53R270HWAPCre mice to different insulin-like molecules (regular insulin, insulin glargine, insulin X10 (of AspB10), IGF1 or vehicle solution). Due to the mammary gland specific p53 mutation the p53R270HWAPCre mice will develop spontanously human like mammary gland tumors in about a year. We found that frequent injections to insulin like molecules decreased the mammary gland tumor latency time in this model. Next we mRNA seqeunced tumors to reveal the underlying mechanisms for the increased tumor progression. For the next generation experiment we isolated mRNA from 50 tumors (10 tumors of each stimulation group) and sequenced with the IonTorrent (40 mil reads, on average 100 bp reads) Overall design: RNA expression profiles of 50 mammary gland tumors were analyzed, 10 tumors per treatment group (chronic insulin, glargine, x10, IGF1 or vehicle exposure)
Publication Title
Insulin-like growth factor 1 receptor activation promotes mammary gland tumor development by increasing glycolysis and promoting biomass production.
Sample Metadata Fields
Specimen part, Cell line, Subject
View Samples- Homo sapiens
- 6 Downloadable Samples
- Affymetrix Human Exon 1.0 ST Array [probe set (exon) version (huex10st)
Description
Differential gene expression in preimplantation embryos has been documented, but few focused studies have been done to compare differential expression in human embryos after embryonic genome activation and specifically how they relate to blastocyst development. We hypothesized that blastocyst stage embryos would differentially express genes in pathways important in cell division, mobilization, and processes important in embryo implantation including endometrial apposition, adhesion, and invasion. We analyzed gene expression in 6 preimplantation human embryos.
Publication Title
Differentially expressed genes in preimplantation human embryos: potential candidate genes for blastocyst formation and implantation.
Sample Metadata Fields
Specimen part
View Samples- Saccharomyces cerevisiae
- 50 Downloadable Samples
- Illumina HiSeq 2500
Description
Transcriptome of S. cerevisiae in shifts between glucose and maltose media with different re-growth conditions Overall design: Cells are pregrown in maltose, then grown for different durations in glucose and then washed back to maltose
Publication Title
A new protocol for single-cell RNA-seq reveals stochastic gene expression during lag phase in budding yeast.
Sample Metadata Fields
Subject
View Samples- Saccharomyces cerevisiae
- 18 Downloadable Samples
- Affymetrix Yeast Genome 2.0 Array (yeast2)
Description
When grown on solid substrates, different microorganisms often form colonies with very specific morphologies. Whereas the pioneers of microbiology often used colony morphology to discriminate between species and strains, the phenomenon has not received much recent attention. In this study, we use a genome-wide assay in the model yeast Saccharomyces cerevisiae to identify all genes that affect colony morphology. We show that several major signaling cascades, including the MAPK, TORC, SNF1 and RIM101 pathways play a role, indicating that morphological changes are a reaction to changing environments. Other genes that affect colony morphology are involved in protein sorting and epigenetic regulation. Interestingly, the screen reveals only few genes that are likely to play a direct role in establishing colony morphology, one notable exception being FLO11, a gene encoding a cell-surface adhesin that has already been implicated in colony morphology, biofilm formation, and invasive and pseudohyphal growth. Using a series of modified promoters to tune FLO11 expression, we confirm the central role of Flo11 and show that differences in FLO11 expression result in distinct colony morphologies. Together, our results provide a first comprehensive looks at the complex genetic network that underlies the diversity in the morphologies of yeast colonies.
Publication Title
Identification of a complex genetic network underlying Saccharomyces cerevisiae colony morphology.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 8 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
In response to elevated glucocorticoid levels, erythroid progenitors rapidly expand to produce large numbers of young erythrocytes. Previous work demonstrates hematopoietic changes in rodents exposed to various physical and psychological stressors, however, the effects of chronic psychological stress on erythropoiesis has not be delineated. We employed laboratory, clinical and genomic analyses of a murine model of chronic restraint stress (RST) to examine the influence of psychological stress on erythropoiesis. Mice exposed to RST demonstrated markers of early erythroid expansion involving the glucocorticoid receptor. In addition, these RST-exposed mice had increased numbers of circulating reticulocytes and increased erythropoiesis in primary and secondary erythroid tissues. Mice also showed increases in erythroid progenitor populations and elevated expression of the erythroid transcription factor KLF1 in these cells. Together this work describes some of the first evidence of psychological stress affecting erythroid homeostasis through glucocorticoid stimulation and begins to define the transcription factor pathway involved.
Publication Title
Chronic restraint stress upregulates erythropoiesis through glucocorticoid stimulation.
Sample Metadata Fields
Sex
View Samples- Saccharomyces cerevisiae
- 24 Downloadable Samples
- Illumina HiSeq 2000
Description
The behavior of yeast cells during industrial processes such as the production of beer, wine and bioethanol has been extensively studied. By contrast, our knowledge about yeast physiology during solid state processes, such as bread dough, cheese or cocoa fermentation remains limited. We investigated changes in the transcriptome of three genetically distinct Saccharomyces cerevisiae strains during bread dough fermentation. Our results show that regardless of the genetic background, all three strains exhibit similar changes in expression patterns. At the onset of fermentation, expression of glucose-regulated genes changes dramatically, and the osmotic stress response is activated. The middle fermentation phase is characterized by the induction of genes involved in amino acid metabolism. Finally, at the latest time point, cells suffer from nutrient depletion and activate pathways associated with starvation and stress response. Further analysis shows that genes regulated by the High Osmolarity Glycerol (HOG) pathway, the major pathway involved in the response to osmotic stress and glycerol homeostasis, are among the most differentially expressed genes at the onset of fermentation. More importantly, deletion of HOG1 and other genes of this pathway significantly reduces fermentation capacity. Together, our results demonstrate that cells embedded in a solid matrix such as bread dough suffer severe osmotic stress, and that a proper induction of the HOG pathway is critical for an optimal fermentation.
Publication Title
Dynamics of the Saccharomyces cerevisiae transcriptome during bread dough fermentation.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 102 Downloadable Samples
- Affymetrix Human Gene 2.1 ST Array (hugene21st)
Description
Inverse and erythrodermic psoriasis are rare subtypes of psoriasis. Whereas the former is characterized by shiny erythematous non-scaly plaques in the body folds, the latter has widespread redness with fine scale, covering over 80% of the body-surface area, and can be life-threatening. Both are considered to be clinical subtypes of chronic plaque psoriasis, and often co-exist or evolve from plaque psoriasis (Boyd and Menter, 1989; Omland and Gniadecki, 2015), but the pathogenic mechanisms involved are unknown, and current treatments are frequently unsatisfactory. To assess shared and unique processes between chronic plaque, inverse, and erythrodermic psoriasis we analyzed archived formalin-fixed paraffin-embedded biopsies of clinically and histologically confirmed chronic plaque (n=12), inverse (n=40) and erythrodermic psoriasis cases (n=30) and healthy control skin (n=20) using Affymetrix ST 2.1 Arrays. Compared with healthy skin, psoriatic plaque lesions yielded 2450 differentially expressed genes (DEGs) (FDR, p<0.05), inverse psoriasis lesions yielded 408 DEGs (FDR, p<0.05) and erythrodermic psoriasis lesions yielded 447 DEGs (FDR, p<0.05). In total 294 genes were found to be shared among the three disease subtypes (FDR, p<0.05). While the overlap only accounted for 12% of the DEGs in chronic plaque psoriasis, it accounted for 66% and 72% of DEGs in erythrodermic and inverse psoriasis respectively.
Publication Title
IL-17 Responses Are the Dominant Inflammatory Signal Linking Inverse, Erythrodermic, and Chronic Plaque Psoriasis.
Sample Metadata Fields
Specimen part, Disease, Disease stage
View Samples