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GSE20972
Glycine max
12 Downloadable Samples
Affymetrix Soybean Genome Array (soybean)
Description
Lipo-chitooligosaccharides (LCOs) produced by N2-fixing rhizobacteria initiate host nodule formation. Foliar application of LCOs has been shown to induce stress-related genes under optimal growth conditions. To study the effects of LCO foliar spray under stressed conditions, soybean seedlings grown at optimal temperature were exposed to sub-optimal temperature. After a 5-day acclimation period, the first trifoliolate leaves were sprayed with 10-7 M LCO (NodBj-V (C18:1, MeFuc)) produced by Bradyrhizobium japonicum, and harvested at 0 and 48 h following treatment. Microarray analysis was performed using Affymetrix GeneChip Soybean Genome Arrays. A total of 147 genes were differentially expressed 48 h after LCO treatment, including a number of stress-related genes and transcription factors. In addition, during the 48 h following treatment, hundreds of genes were differentially expressed in LCO-treated plants, indicating that the dynamic soybean foliar transcriptome was highly responsive to LCO treatment. The microarray data was supported by quantitative real-time PCR data.
Publication Title
No associated publication
Sample Metadata Fields
Specimen part, Treatment, Time
View Samples- Caenorhabditis elegans
- 25 Downloadable Samples
Illumina Genome Analyzer II, Illumina Genome Analyzer IIx
Description
In C. elegans, the bilateral Q neuroblasts and their neuronal descendants undergo long-range migrations. QR (on the right) polarizes and migrates anteriorly, whereas QL (on the left) polarizes and migrates posteriorly. The Hox transcription factor MAB-5 is a determinant of this posterior migration of QL, and likely regulates target genes that determine posterior versus anterior migration. We sought to identify these downstream networks of genes via RNA-seq, and identify transcripts that are differentially expressed between wildtype and mab-5 mutant genotypes. We sequenced RNA extracted from early L1 staged animals from four C. elegans genotypes: wildtype worms, mab-5(e1239) and mab-5(gk670) loss-of-function mutants, and the mab-5(e1751) gain-of-function mutant. Tests revealed a number of differentially expressed genes, many of which were validated by subsequent RNAi.
Publication Title
No associated publication
Sample Metadata Fields
Disease, Cell line
View Samples- Drosophila melanogaster
- 12 Downloadable Samples
- Illumina HiSeq 2500
Description
The goal is to identify changes in gene expression with aging in the heads of mated female D. melanogaster. We measured lifespan in mated females from several hundred RILs (Recombinant Inbred Lines) derived from the "B" panel of the DSPR (Drosophila Synthetic Population Resource), additionally sampling young (Day 3) and old (day on which at least 50% of the animals were dead) animals. Subsequently we harvested RNA, specifically from heads (5-10 per strain per sample), from six RILs, for each RIL generating 2 RNA samples (from young and from old females). Each of the 12 total RNA samples was used to construct an Illumina TruSeq RNAseq library, and all 12 libraries were mixed, and run over two PE50 "Rapid Run" HiSeq2500 lanes.
Publication Title
No associated publication
Sample Metadata Fields
Sex, Specimen part, Cell line
View Samples- Drosophila melanogaster
- 4 Downloadable Samples
- Illumina HiSeq 2500
Description
We carried out genetic mapping in the Drosophila Synthetic Population Resource (FlyRILs.org, Genome Research 22:1558-66) to identify QTL (quantitative trait loci) contributing to variation in the nicotine resistance of first-instar larva. To follow up this work, and look for candidate genes exhibiting differential gene expression, we carried out RNAseq on pools of first-instar larvae from two of the inbred strains that founded the DSPR: Lines A3 (derived from Bloomington Stock 3844) and A4 (derived from Bloomington Stock 3852). In addition we exposed groups of larvae from each genotype to nicotine for a short period of time, resulting in four samples: A3-control, A3-nicotine, A4-control, and A4-nicotine. Analysis revealed a number of genes that changed in expression between genotypes and/or treatments.
Publication Title
No associated publication
Sample Metadata Fields
Sex, Specimen part, Cell line, Treatment
View Samples- Drosophila melanogaster
- 4 Downloadable Samples
- Illumina HiSeq 2500
Description
The goal is to identify changes in gene expression with aging in the bodies (thorax plus abdomen) of mated female D. melanogaster. We measured lifespan in mated females from several hundred RILs (Recombinant Inbred Lines) derived from the "B" panel of the DSPR (Drosophila Synthetic Population Resource), additionally sampling young (Day 3) and old (day on which at least 50% of the animals were dead) animals. Subsequently we harvested RNA from subsets of the samples, generating 4 pools of RNA from (a) young animals from short-lived lines, (b) old animals from short-lived lines, (c) young animals from long-lived lines, and (d) old animals from long-lived lines. Each pool was used to construct an Illumina TruSeq RNAseq library, all 4 libraries were mixed, and run over a single SR100 HiSeq2500 lane.
Publication Title
No associated publication
Sample Metadata Fields
Sex, Specimen part, Cell line
View Samples- Mus musculus
- 5 Downloadable Samples
- Illumina Genome Analyzer
Description
Next Generation Sequencing Analysis of Wild Type and Mist1-/- Pancreatic Transcriptomes
Publication Title
No associated publication
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 1 Downloadable Sample
- Illumina HumanHT-12 V4.0 expression beadchip
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
A common promoter hypomethylation signature in invasive breast, liver and prostate cancer cell lines reveals novel targets involved in cancer invasiveness.
Sample Metadata Fields
Sex, Disease, Disease stage, Cell line
View Samples- Homo sapiens
- 1 Downloadable Sample
- Illumina HumanHT-12 V4.0 expression beadchip
Description
Cancer invasion and metastasis is the most morbid aspect of cancer and is governed by different cellular mechanisms than those driving the deregulated growth of tumors. We addressed here the question of whether a common DNA methylation signature of invasion exists in cancer cells from different origins that differentiates invasive from noninvasive cells. We identified a common DNA methylation signature consisting of hyper- and hypomethylation and determined the overlap of differences in DNA methylation with differences in mRNA expression using expression array analyses. A pathway analysis reveals that the hypomethylation signature includes some of the major pathways that were previously implicated in cancer migration and invasion such as TGF beta and ERBB2 triggered pathways. The relevance of these hypomethylation events in human tumors was validated by identification of the signature in several publicly available databases of human tumor transcriptomes. We shortlisted novel invasion promoting candidates and tested the role of four genes from the list C11orf68, G0S2, SHISA2 and TMEM156 in invasiveness using siRNA depletion. Importantly these genes are upregulated in human cancer specimens as determined by immunostaining of human normal and cancer breast, liver and prostate tissue arrays. Since these genes are activated in cancer they constitute a group of targets for specific pharmacological inhibitors of cancer invasiveness.
Publication Title
A common promoter hypomethylation signature in invasive breast, liver and prostate cancer cell lines reveals novel targets involved in cancer invasiveness.
Sample Metadata Fields
Sex, Disease, Disease stage, Cell line
View Samples- Homo sapiens
- 237 Downloadable Samples
- Illumina humanRef-8 v2.0 expression beadchip
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
Global analysis of the impact of environmental perturbation on cis-regulation of gene expression.
Sample Metadata Fields
Sex, Specimen part, Time
View Samples- Homo sapiens
- 422 Downloadable Samples
- Affymetrix Human Transcriptome Array 2.0 (hta20)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
Effect of Human Genetic Variability on Gene Expression in Dorsal Root Ganglia and Association with Pain Phenotypes.
Sample Metadata Fields
Specimen part
View Samples