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SRP047307
Homo sapiens
3 Downloadable Samples
IlluminaHiSeq2500
Description
RNA-Seq study from Caco2 cells following transduction with control shRNA and shRNA against CHD6
Publication Title
No associated publication
Sample Metadata Fields
No sample metadata fields
View Samples- Vitis vinifera
- 27 Downloadable Samples
Affymetrix Vitis vinifera (Grape) Genome Array (vitisvinifera)
Description
Global gene expression analysis of grapevine cv. Pinot Noir berries during development and ripening. Time-course comparison of samples collected at three developmental stages (stages 33, 34 and 36 according to the modified E-L system, ref: Coombe BG, Aust J Grape Wine Res 1995, 1: 104-110) during three seasons (2003, 2005 and 2006).
Publication Title
Genome-wide transcriptional analysis of grapevine berry ripening reveals a set of genes similarly modulated during three seasons and the occurrence of an oxidative burst at vèraison.
Sample Metadata Fields
Age, Specimen part, Time
View Samples- 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.
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
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.
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
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
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.
Sample Metadata Fields
No sample metadata fields
View Samples- Caenorhabditis elegans
- 4 Downloadable Samples
- Illumina HiSeq 2000
Description
Deep sequencing of RNA isolated from ALT survivors in N2 genetic backgrounds (CS, NS). RNA-seq data was compared to the parental strain N2 trt-1(ok410). Total RNA was extracted from synchronized L4 stage worms.
Publication Title
No associated publication
Sample Metadata Fields
Sex, Specimen part, Disease, Cell line
View Samples- Zea mays
- 41 Downloadable Samples
- Illumina HiSeq 4000
Description
Senescence has tremendous impact on yield and nutritional quality of agricultural produce. However, scant information is available on genetic architecture of senescence in maize (Zea mays L.) despite the importance of stay-green, a delayed senescence phenotype, in this major cereal crop. We combined different approaches including co-expression networks derived from time-course transcriptome analysis of senescence and stay-green to identify unique candidate genes.
Publication Title
No associated publication
Sample Metadata Fields
Specimen part
View Samples