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Homo sapiens
99 Downloadable Samples
Affymetrix Human Genome U133A 2.0 Array (hgu133a2)
Description
Pediatric acute lymphoblastic leukemia (ALL) contains cytogenetically distinct subtypes that respond differently to cytotoxic drugs. Subtype classification can be also achieved through gene expression profiling. However, how to apply such classifiers to a single patient and correctly diagnose the disease subtype in an independent patient group has not been addressed. Furthermore, the underlying regulatory mechanisms responsible for the subtype-specific gene expression patterns are still largely unknown. Here, by combining three published microarray datasets (PMIDs: 12086872, 12730115, 17002788) on 535 Caucasian samples and generating a new dataset on 100 Chinese children ALL samples, we were able to 1) identify a 62-gene classifier with 97.6% accuracy from the Caucasian samples and validated it on the completely independent set of 100 Chinese samples, 2) to uncover potential regulatory networks of ALL subtypes. The classifier we identified was so far the only one that could be applied directly to a single sample and sustained validation in a large independent patient group. Our results also suggest that the etiology of ALL is largely the same among different ethnic groups, and that the transcription factor hubs in the predicted regulatory network might play important roles in regulating gene expression and development of ALL.
Publication Title
Gene expression-based classification and regulatory networks of pediatric acute lymphoblastic leukemia.
Alternate Accession IDs
Sample Metadata Fields
Specimen part, Disease, Race
View Samples- Oryza sativa
- 14 Downloadable Samples
- Affymetrix Rice Genome Array (rice)
Description
Ethylene plays major roles in adaptive growth of rice plants in water-saturated soil; however, ethylene signaling in rice is largely unclear. Here, we report identification and characterization of ethylene-response mutants based on distinct ethylene-response phenotypes of dark-grown rice seedlings.
Publication Title
No associated publication
Alternate Accession IDs
Sample Metadata Fields
Specimen part, Treatment
View Samples- Homo sapiens
- 9 Downloadable Samples
Illumina HiSeq 2000
Description
Recent studies have demonstrated that human astrocytes and fibroblasts can be directly converted into functional neurons by small molecules. However, the reported reprogramming efficiency of human fibroblasts is extremely low, resulting in limited clinical application for the treatment of neurological disorders. Here, we report that human fibroblasts can be efficiently and directly reprogrammed into functional neuron-like cells (with a yield up to 82% TUJ1-positive neuron-like cells) by serially exposing cells to a combination of small molecules. These chemically induced neurons (iNs) displayed typical neuronal morphologies and showed neuronal transcriptional networks resembling human primary embryonic brain neurons. The iNs also exhibited mature firing patterns and formed functional synapse when cultured on mouse astrocytes. Importantly, the iNs can survive, mature and integrate into local circuits after transplantation into the postnatal mouse brains. Our study provides a rapid and efficient transgene-free approach for chemically generating neuron-like cells from human fibroblasts. Further, our approach offers strategies for disease modeling and drug discovery in central nervous system disorders.
Publication Title
Rapid and Efficient Conversion of Human Fibroblasts into Functional Neurons by Small Molecules.
Alternate Accession IDs
None
Sample Metadata Fields
Sex, Specimen part
View Samples- Oryza sativa
- 7 Downloadable Samples
- Affymetrix Rice Genome Array (rice)
Description
Receptor-like kinases (RLKs) play important roles in plant development and defense responses; however, their functions in other processes remain unclear. Here, we report that OsSIK2, an S-domain RLK from rice, is involved in abiotic stress and senescence process, integrating stress signals into developmental program for adaptive growth.
Publication Title
No associated publication
Alternate Accession IDs
Sample Metadata Fields
Specimen part
View Samples- Oryza sativa
- 6 Downloadable Samples
- Affymetrix Rice Genome Array (rice)
Description
Ethylene plays major roles in adaptive growth of rice plants in water-saturated soil; however, ethylene signaling in rice is largely unclear. Here, we report identification and characterization of ethylene-response mutants based on distinct ethylene-response phenotypes of dark-grown rice seedlings.
Publication Title
No associated publication
Alternate Accession IDs
Sample Metadata Fields
Specimen part, Treatment
View Samples- Arabidopsis thaliana
- 4 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
In plants, fatty acids are de novo synthesized predominantly in plastids fromacetyl-CoA. Although fatty acid biosynthesis has been biochemically well-studied, little isknown about the regulatory mechanisms of the pathway. Here, we show that overexpressionof the Arabidopsis (Arabidopsis thaliana) LEAFY COTYLEDON1 (LEC1) gene causesglobally increased expression of fatty acid biosynthetic genes, which are involved in keyreactions of condensation, chain elongation and desaturation of fatty acid biosynthesis. Inthe plastidial fatty acid synthetic pathway, over 58% of known enzyme-coding genes areupregulated in LEC1-overexpressing transgenic plants, including those encoding threesubunits of acetyl-CoA carboxylase, a key enzyme controlling the fatty acid biosynthesisflux. Moreover, genes involved in glycolysis and lipid accumulation are also upregulated.Consistent with these results, levels of major fatty acid species and lipids were substantiallyincreased in the transgenic plants. Genetic analysis indicates that the LEC1 function ispartially dependent on ABSCISIC ACID INSENSITIVE3, FUSCA3 and WRINKLED1 in theregulation of fatty acid biosynthesis. Moreover, a similar phenotype was observed intransgenic Arabidopsis plants overexpressing two LEC1-like genes of Brassica napus.These results suggest that LEC1 and LEC1-like genes act as key regulators to coordinate theexpression of fatty acid biosynthetic genes, thereby representing a promising target forgenetic improvement of oil-production plants.
Publication Title
LEAFY COTYLEDON1 is a key regulator of fatty acid biosynthesis in Arabidopsis.
Alternate Accession IDs
Sample Metadata Fields
No sample metadata fields
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E-MTAB-381- Danio rerio
- 40 Downloadable Samples
- Affymetrix Zebrafish Genome Array (zebrafish)
Description
Transcriptional profiling of light response in the zebrafish at several organizational levels: the whole animal, the organ and the cell. Exposure of larvae, heart organ cultures and cell culture cells to light pulses of 1 and 3 hours duration and measurement of changes in gene expression compared to controls kept in the dark.
Publication Title
The light induced transcriptome of the zebrafish
Alternate Accession IDs
None
Sample Metadata Fields
Specimen part, Cell line, Time
View Samples- Oryza sativa
- 37 Downloadable Samples
- Affymetrix Rice Genome Array (rice)
Description
Plant diurnal oscillation is a 24-hour period based variation. The correlation between diurnal genes and biological pathways was widely revealed by microarray analysis in different species. Rice (Oryza sativa) is the major food staple for about half of the world's population. The rice flag leaf is essential in providing photosynthates to the grain filling. However, there is still no comprehensive view about the diurnal transcriptome for rice leaves. In this study, we applied rice microarray to monitor the rhythmically expressed genes in rice seedling and flag leaves. We developed a new computational analysis approach and identified 6,266 (10.96%) diurnal probe sets in seedling leaves, 13,773 (24.08%) diurnal probe sets in flag leaves. About 65% of overall transcription factors were identified as flag leaf preferred. In seedling leaves, the peak of phase distribution was from 2:00am to 4:00am, whereas in flag leaves, the peak was from 8:00pm to 2:00am. The diurnal phase distribution analysis of gene ontology (GO) and cis-element enrichment indicated that, some important processes were waken by the light, such as photosynthesis and abiotic stimulus, while some genes related to the nuclear and ribosome involved processes were active mostly during the switch time of light to dark. The starch and sucrose metabolism pathway genes also showed diurnal phase. We conducted comparison analysis between Arabidopsis and rice leaf transcriptome throughout the diurnal cycle. In summary, our analysis approach is feasible for relatively unbiased identification of diurnal transcripts, efficiently detecting some special periodic patterns with non-sinusoidal periodic patterns. Compared to the rice flag leaves, the gene transcription levels of seedling leaves were relatively limited to the diurnal rhythm. Our comprehensive microarray analysis of seedling and flag leaves of rice provided an overview of the rice diurnal transcriptome and indicated some diurnal regulated biological processes and key functional pathways in rice.
Publication Title
Transcriptome phase distribution analysis reveals diurnal regulated biological processes and key pathways in rice flag leaves and seedling leaves.
Alternate Accession IDs
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 17 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
Dietary interventions are effective ways to extend or shorten lifespan. By examining midlife hepatic gene expressions in mice under different dietary conditions, which resulted in different lifespans and aging-related phenotypes, we were able to identify genes and pathways that modulate the aging process. We found that pathways transcriptionally correlated with diet-modulated lifespan and physiological changes were enriched for lifespan-modifying genes.
Publication Title
Midlife gene expressions identify modulators of aging through dietary interventions.
Alternate Accession IDs
Sample Metadata Fields
Sex, Age, Specimen part
View Samples- Gossypium hirsutum
- 17 Downloadable Samples
- Affymetrix Cotton Genome Array (cotton)
Description
Abiotic stress is a major environmental factor that limits cotton growth and yield, moreover, this problem has become more and more serious recently and multiple stresses often occur simultaneously due to the global climate change and environmental pollution.
Publication Title
Transcriptome analysis reveals crosstalk of responsive genes to multiple abiotic stresses in cotton (Gossypium hirsutum L.).
Alternate Accession IDs
Sample Metadata Fields
Specimen part
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