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E-MEXP-998
Saccharomyces cerevisiae
24 Downloadable Samples
Affymetrix Yeast Genome 2.0 Array (yeast2)
Description
Yeast cells were grown up in SD media containing all required amino acids. Each strain set was performed in triplicate. One set had no changes, the second set had 1mM methionine supplenting the media for the duration of growth and the third set was exposed to 0.5mM hydrogen peroxide for 15 minutes prior to harvesting
Publication Title
Gcn4 is required for the response to peroxide stress in the yeast Saccharomyces cerevisiae.
Sample Metadata Fields
Compound
View Samples- Saccharomyces cerevisiae
- 18 Downloadable Samples
- Affymetrix Yeast Genome S98 Array (ygs98)
Description
Global restriction of protein synthesis is a hallmark of cellular stress. Using hydrogen peroxide, we monitor the transcript level and also the translation status for each RNA using cycloheximide to freeze elongating ribosomes. Polyribosome fractionation of cell extracts was used to separate highly translated and poorly translated mRNAs that were then separately analysed.
Publication Title
Global translational responses to oxidative stress impact upon multiple levels of protein synthesis.
Sample Metadata Fields
Sex, Compound
View Samples- Mus musculus
- 24 Downloadable Samples
- Affymetrix Mouse Clariom S Array (clariomsmouse)
Description
The intestinal epithelium constitutes a crucial defense to the potentially life-threatening effects of gut microbiota. However, due to a complex underlying vasculature, hypoperfusion and resultant tissue ischemia pose a particular risk to function and integrity of the epithelium. The small ubiquitin-like modifier (SUMO) conjugation pathway critically regulates adaptive responses to metabolic stress and is of particular significance in the gut, as inducible knockout of the SUMO-conjugating enzyme Ubc9 results in rapid intestinal epithelial disintegration. Here we analyzed the pattern of individual SUMO isoforms in intestinal epithelium and investigated their roles in intestinal ischemia/reperfusion (I/R) damage. Immunostaining revealed that epithelial SUMO2/3 expression was almost exclusively limited to crypt epithelial nuclei in unchallenged mice. However, intestinal I/R or overexpression of Ubc9 caused a remarkable enhancement of epithelial SUMO2/3 staining along the crypt-villus axis. Unexpectedly, a similar pattern was found in SUMO1 knockout mice. Ubc9 transgenic mice, but also SUMO1 knockout mice were protected from I/R injury as evidenced by better preserved barrier function and blunted inflammatory responses. PCR array analysis of microdissected villus-tip epithelia revealed a specific epithelial contribution to reduced inflammatory responses in Ubc9 transgenic mice, as key chemotactic signaling molecules such as IL17A were significantly downregulated. Together, our data indicate a critical role particularly of the SUMO2/3 isoforms in modulating responses to I/R and provide the first evidence that SUMO1 deletion activates a compensatory process that protects from ischemic damage.
Publication Title
Ubc9 overexpression and SUMO1 deficiency blunt inflammation after intestinal ischemia/reperfusion.
Sample Metadata Fields
Treatment
View Samples- Caenorhabditis elegans
- 8 Downloadable Samples
Illumina HiSeq 4000
Description
Cellular differentiation requires both activation of target cell programs and repression of non-target cell programs. Transcriptional repressors such as RE1-silencing transcription factor (REST) and Hairy/Enhancer of Split (Hes) repress neuronal genes in non-neuronal cells. However, it is unknown whether transcriptional repressors of non-neuronal genes in neuronal precursors are required to specify neuronal fate during development. The Myt1 family of zinc finger transcription factors contributes to fibroblast to neuron reprogramming in vitro by repressing Notch signaling. Here, we show that ztf-11 (Zinc-finger Transcription Factor-11), the sole Caenorhabditis elegans Myt1 homolog, is required for neurogenesis in multiple neuronal lineages, including an in vivo developmental epithelial-to-neuronal transdifferentiation event. ztf-11 is exclusively expressed in all neuronal precursors with remarkable specificity at single cell resolution. Loss of ztf-11 leads to upregulation of non-neuronal genes and reduced neurogenesis. Ectopic expression of ztf-11 in epidermal lineages is sufficient to produce additional neurons. Our genetic and genomic experiments show that ZTF-11 indeed functions as a transcriptional repressor to suppress the activation of non-neuronal genes in neurons; however, it does not function via repression of Notch signaling. Instead, ZTF-11 binds to the MuvBco-repressor complex, which we show is also required for neurogenesis. These results dovetail with ability of Myt1l (Myt1-like) to drive neuronal transdifferentiation in vitro in vertebrate systems. Together, we identified an evolutionarily conserved mechanism to specify neuronal cell fate by repressing non-neuronal genes. Overall design: 4 biological replicates each under 2 experemental conditions (ztf-11 KD and negative control) were used for total of 8 samples
Publication Title
A Myt1 family transcription factor defines neuronal fate by repressing non-neuronal genes.
Sample Metadata Fields
Specimen part, Cell line, Treatment, Subject
View Samples- Caenorhabditis elegans
- 5 Downloadable Samples
- Illumina HiSeq 4000
Description
We sorted approx. 10000 neurons per sample from day one adult worms. We collected two wildtype samples and three thoc-5(wy822) mutant samples. Overall design: RNAseq of FACS-sorted C.elegans neurons from wildtype and thoc-5(wy822) mutant animals.
Publication Title
The THO Complex Coordinates Transcripts for Synapse Development and Dopamine Neuron Survival.
Sample Metadata Fields
Specimen part, Subject
View Samples- Homo sapiens
- 81 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
Microarray analyses for the identification of differences in gene expression patterns have increased our understanding of the molecular genetic events in colorectal cancer.
Publication Title
A molecular signature for the prediction of recurrence in colorectal cancer.
Sample Metadata Fields
Sex
View Samples- Rattus norvegicus
- 6 Downloadable Samples
- Affymetrix Rat Genome 230 2.0 Array (rat2302)
Description
Various pluripotent stem (PS) cells can be isolated from early developing embryos in mouse. Among these, two kinds of PS cells were isolated from mouse blastocysts: conventional embryonic stem (ES) cells with domed morphology that are maintained with LIF and BMP for self-renewal, and FAB-ES cells with flat morphology that need bFGF, activinA and BIO for self-renewal. Here, we report a novel PS cell line from rat blastocysts, which is distinguishable from conventional ES cells but is morphologically similar to mouse epiblast stem cell (EpiSC) lines. We used microarrays to detail the global program of gene expression of rES and rPS.
Publication Title
The heterogeneity and dynamic equilibrium of rat embryonic stem cells.
Sample Metadata Fields
Specimen part
View Samples- Mus musculus
- 3 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
Damage-associated molecular pattern (DAMP) molecules S100A8 and S100A9 with well-known functions in inflammation, tumor growth and metastasis. It has been found to have promote tumor cell proliferation activity at low concentration . However, the mechanism underlying this remains unclear. In the current study, we performed genome expression profiling analysis using the Affymetrix genome wide microarray system to identify broad scale changes in gene expression associated with S100a8 or S100a9 recombinant protein stimulation in murine colon carcinoma cell line CT26.WT.
Publication Title
Inflammation-induced S100A8 activates Id3 and promotes colorectal tumorigenesis.
Sample Metadata Fields
Cell line
View Samples- Homo sapiens
- 12 Downloadable Samples
- Affymetrix Human Gene 1.0 ST Array (hugene10st)
Description
YAP knockdown in HUVEC elicits proliferation and cell cycle preogression defects. YAP deficient cells caused arrest in G1 and defects in S-phase entry. The microarray analysis was conducted to identify potential YAP targets that are involved in HUVEC cell cycle regulation
Publication Title
YAP regulates S-phase entry in endothelial cells.
Sample Metadata Fields
Specimen part, Treatment
View Samples- Mus musculus
- 9 Downloadable Samples
- Affymetrix Mouse Gene 1.0 ST Array (mogene10st)
Description
Dgcr8 and Dicer are both important components of the microRNA biogenesis pathway while Dicer is also implicated in biogenesis of other types of small RNAs such as siRNAs and mirtrons. Here we performed microarray analysis of WT, Dgcr8 and Dicer knockout ES cells to identify mRNAs differentially regulated upon loss of Dgcr8 and Dicer.
Publication Title
Genomic analysis suggests that mRNA destabilization by the microprocessor is specialized for the auto-regulation of Dgcr8.
Sample Metadata Fields
Specimen part
View Samples