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E-MEXP-3713
Arabidopsis thaliana
18 Downloadable Samples
Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
Microarray experiments were performed using Arabidopsis wild type plants (Col-0) and srk2dei triple knockout mutant to investigate the functions of ABA-activated protein kinases, SRK2D/SnRK2.2, SRK2E/OST1 and SRK2I/SnRK2.3. Transcription profiles of wild type and mutants were compared under ABA treatment or dehydration stress for 0 and 90 min. The srk2dei mutant was established by crossing T-DNA insertion mutants provided from Arabidopsis Biological Resource Center.
Publication Title
Genetics and phosphoproteomics reveal a protein phosphorylation network in the abscisic acid signaling pathway in Arabidopsis thaliana
Sample Metadata Fields
Age, Specimen part
View Samples- Mus musculus
- 51 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
Transcriptiome analysis is an excellent approach to understand the mechanism underlying nuclear reprogramming in somatic-cell-cloned embryos. Analysis of the transcriptomic data from the oocyte to blastocyst stage revealed that specific genes were inappropriately reprogrammed at each stage. Sertoli cell-cloned embryos appear to develop normally because the progression of incorrect reprogramming is concealed throughout development.
Publication Title
The transcriptomic architecture of mouse Sertoli cell clone embryos reveals temporal–spatial-specific reprogramming.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 6 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
The oocytes of B6.Y(TIR) sex-reversed female mouse mature in culture but fail to develop after fertilization because of their cytoplasmic defects. To identify the defective components, we compared the gene expression profiles between the fully-grown oocytes of B6.Y(TIR) (XY) females and those of their XX littermates by cDNA microarray. 173 genes were found to be higher and 485 genes were lower in XY oocytes than in XX oocytes by at least 2-fold. We compared the transcript levels of selected genes by RT-PCR in XY and XX oocytes, as well as in XO oocytes missing paternal X-chromosomes. All genes tested showed comparable transcript levels between XX and XO oocytes, indicating that mRNA accumulation is well adjusted in XO oocytes. By contrast, in addition to Y-encoded genes, many genes showed significantly different transcript levels in XY oocytes. We speculate that the presence of the Y-chromosome, rather than the absence of the second X-chromosome, caused dramatic changes in the gene expression profile in the XY fully-grown oocyte.
Publication Title
No associated publication
Sample Metadata Fields
Specimen part
View Samples- Rattus norvegicus
- 10 Downloadable Samples
- Affymetrix Rat Genome 230 2.0 Array (rat2302)
Description
To investigate effects of intake of mulberry leaves on hyperlipidemia, we performed gene expression profiling on rat liver by microarray analysis.
Publication Title
Ameliorative effects of mulberry (Morus alba L.) leaves on hyperlipidemia in rats fed a high-fat diet: induction of fatty acid oxidation, inhibition of lipogenesis, and suppression of oxidative stress.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 12 Downloadable Samples
- Affymetrix Mouse Gene 1.0 ST Array (mogene10st)
Description
Individual olfactory sensory neurons express a single odorant receptor (OR) gene from either class I genes residing in a single cluster on a single chromosome or class II genes spread over multiple clusters on multiple chromosomes.
Publication Title
A long-range cis-regulatory element for class I odorant receptor genes.
Sample Metadata Fields
Sex, Specimen part
View Samples- Mus musculus
- 11 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
Each olfactory sensory neuron (OSN) chooses a single odorant receptor (OR) gene from the class I or class II OR repertoire in mice. We have found that the transcription factor Bcl11b, which is coexpressed with class II OR genes both in frog and mouse, determines the class of OR to be expressed in OSNs. Both loss- and gain-of-function analyses demonstrate that Bcl11b is necessary for class II genes expression, by suppressing the class I-specific enhancer. Overall, we identified a unique transcriptional mechanism that serves as a binary switch for the OR class choice that is likely to have contributed to the acquisition of terrestrial-specific class II OR expression.
Publication Title
No associated publication
Sample Metadata Fields
Sex, Specimen part
View Samples- Danio rerio
- 6 Downloadable Samples
- Affymetrix Zebrafish Genome Array (zebrafish)
Description
The Spt4-Spt5 complex, and its human homolog DSIF (DRB sensitivity-inducing factor), is unique in its ability to regulate Pol II processivity. Previous studies have shown that Spt5 has the characteristics of a general transcription-elongation factor. However, mutagenesis of Spt5 showed specific phenotypes during development, which were far less severe than those of Pol II defects or TBP deficient embryos. It seems paradoxical that a mutation which alters a general elongation factor can cause rather specific developmental defects. By using Spt5 knockdown zebrafish embryos and microarrays, here we showed that transcript abundance for only a small subset of genes is altered by loss of Spt5. Further investigation of the down-regulated genes showed that the genes most intensely repressed by the knockdown were strongly activated during early development in untreated embryos. Thus, this study shows that gene activation levels may create different requirements for Pol II processivity. Active transcription requires Spt5 for efficient elongation through its stimulatory activity on Pol II processivity.
Publication Title
Erythropoiesis is regulated by the transcription elongation factor Foggy/Spt5 through gata1 gene regulation.
Sample Metadata Fields
Age
View Samples- Sus scrofa
- 8 Downloadable Samples
Illumina HiSeq 2500
Description
Gene expression was examined in granulosa cells and oocytes in various stage of follicle and in vitro grown oocytes and granulosa cells complexes in sus scrofa.
Publication Title
Gene expression patterns in granulosa cells and oocytes at various stages of follicle development as well as in in vitro grown oocyte-and-granulosa cell complexes.
Sample Metadata Fields
Specimen part
View Samples- Mus musculus
- 4 Downloadable Samples
- Illumina HiSeq 2500
Description
In mice, primordial germ cells (PGCs), which are the precursors of gametes, are fate-determined from pluripotent epiblasts. The epigenetic regulation of PGC fate determination remains poorly understood. We identify histone deacetylase 3 (HDAC3) as an epigenetic regulator of PGC fate determination by an RNA interference screen for histone modifier genes involved in PGC-like cell (PGCLC) induction in culture. To comprehensively investigate changes in gene expression following Hdac3-KD during PGCLC induction, we carried out RNA sequencing (RNA-seq) analysis to compare the transcriptome of the Hdac3-KD cells with that of the control KD cells 2 days after induction of PGCLCs.
Publication Title
No associated publication
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 6 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
Acetylation and deacetylation of histones and other proteins depend on the opposing activities of histone acetyltransferases and histone deacetylases (HDACs), leading to either positive or negative gene expression changes. The use of HDAC inhibitors (HDACi) has uncovered a role for HDACs in the control of proliferation, apoptosis and inflammation. However, little is known of the roles of specific HDACs in intestinal epithelial cells (IEC). We investigated the consequences of ablating both Hdac1 and Hdac2 in murine IECs gene expression.
Publication Title
HDAC1 and HDAC2 restrain the intestinal inflammatory response by regulating intestinal epithelial cell differentiation.
Sample Metadata Fields
Specimen part
View Samples