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GSE26208
Glycine max
6 Downloadable Samples
Affymetrix Soybean Genome Array (soybean)
Description
The seed coat of black (iRT) soybean with the dominant R allele begins to accumulate cyanic pigments at the transition stage of seed development (300 400 mg fresh seed weight), whereas the brown (irT) nearly-isogenic seed coat with the recessive r allele lacks cyanic pigments at all stages of seed development.
Publication Title
Combined analysis of transcriptome and metabolite data reveals extensive differences between black and brown nearly-isogenic soybean (Glycine max) seed coats enabling the identification of pigment isogenes.
Sample Metadata Fields
Specimen part
View Samples- Rattus norvegicus
- 2 Downloadable Samples
- Affymetrix Rat Genome 230 2.0 Array (rat2302)
Description
AT6.1 cells transfected to over-express Ndrg-1 were compared with AT6.1 vector control cells in a microarray analysis. The aim of the study was to identify differentially expressed genes between the two cell lines, as these may be modulated by Ndrg-1.
Publication Title
The iron-regulated metastasis suppressor, Ndrg-1: identification of novel molecular targets.
Sample Metadata Fields
Cell line
View Samples- Homo sapiens
- 40 Downloadable Samples
- Affymetrix Human Genome U133A Array (hgu133a)
Description
End stage renal disease (ESRD) is associated with hyperplastic-cystic remodelling of the kidneys (ARCD) and increased rate of kidney tumours. Using the Affymetrix oligoarray, we have established the gene expression signature of ESRD/ARCD kidneys and compared to those of normal kidneys and of distinct types of renal tumours.
Publication Title
Gene expression profiling of chromophobe renal cell carcinomas and renal oncocytomas by Affymetrix GeneChip using pooled and individual tumours.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 12 Downloadable Samples
- Affymetrix Mouse Gene 1.0 ST Array (mogene10st)
Description
Parathyroid hormone (PTH) plays an essential role in regulating calcium and bone homeostasis in the adult, but whether PTH is required at all for regulating fetal-placental mineral homeostasis is uncertain. To address this we treated Pth-null mice in utero with 1 nmol PTH (1-84) or saline and examined placental calcium transfer 90 minutes later. It was found that placental calcium transfer increased in Pth-null fetuses treated with PTH as compared to Pth-null fetuses treated with saline. Subsequently, to determine the effect of PTH treatment on placental gene expression, in a separate experiment, 90 minutes after the fetal injections the placentas were removed for subsequent RNA extraction and microarray analysis.
Publication Title
Parathyroid hormone regulates fetal-placental mineral homeostasis.
Sample Metadata Fields
Sex, Specimen part, Treatment
View Samples- Homo sapiens
- 24 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
Background: Prostate cancer is the second leading cause of cancer mortality among US men. Epidemiological evidence suggests that high vitamin D status protects men from prostate cancer and the active form of vitamin D, 1,25 dihydroxyvitamin D3 (1,25(OH)2D) has anti-cancer effects in cultured prostate cells. Still, the molecular mechanisms and the gene targets for vitamin D-mediated prostate cancer prevention are unknown.
Publication Title
1,25 dihydroxyvitamin D-mediated orchestration of anticancer, transcript-level effects in the immortalized, non-transformed prostate epithelial cell line, RWPE1.
Sample Metadata Fields
Specimen part, Cell line, Treatment, Time
View Samples- Mus musculus
- 24 Downloadable Samples
- Affymetrix Mouse Gene 1.0 ST Array (mogene10st)
Description
Dietary lipids and gut microbiota may both influence adipose tissue physiology. By feeding conventional and germ-free mice high fat diets with different lipid compositon we aimed to investigate how dietary lipids and the gut microbiota interact to influence inflammation and metabolism in epididymal adipiose tissue (EWAT)
Publication Title
Crosstalk between Gut Microbiota and Dietary Lipids Aggravates WAT Inflammation through TLR Signaling.
Sample Metadata Fields
Sex, Age, Specimen part
View Samples- Homo sapiens
- 3 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
BRAFV600E remodels the melanocyte transcriptome and induces BANCR to regulate melanoma cell migration.
Sample Metadata Fields
Specimen part, Cell line
View Samples- Gallus gallus
- 4 Downloadable Samples
- Affymetrix Chicken Genome Array (chicken)
Description
Metastatic progression is the leading cause of cancer mortality yet we have an incomplete view of the genetic events governing this process. An investigation was undertaken to explore the role of homeodemain only protein X (HOPX) in metastatic propensity and to identify other genes that may participate in metastasis development. The transcription factor HOPX was assessed for its possible involvement in metastasis formation using a knock-down induced by plasmid-delivered shRNAs. We used our original model system of chicken v-src-transformed tumour cell line PR9692 and its subclone (PR9692-E9) that have lost the ability to induce metastases after inoculation into syngeneic chickens without any significant change in primary tumour formation. We found that also a PR9692 cell line with decreased expression of HOPX gene (PR9692-shHOPX) lost its metastatic capacity in vivo (in chickens) and displayed a reduced cell migration in vitro. We compared the gene expression profiles of control (PR9692-shMOCK) and PR9692-shHOPX cells using oligonucleotide microarrays, assuming that genes with differential expression might be associated with metastasis. The data were compared with a previous study showing differences in gene expression between the PR9692 and PR9692-E9 cells. Bioinformatics was applied to identify gene expression patterns associated with metastasis. 234 genes were identified to show at least 2-fold change in both pairs of cell lines. The results were validated with real-time quantitative RT-PCR and the differential expression was confirmed for several genes. We were also able to demonstrate a significant change at protein level in case of three selected genes (NCAM, FOXG1, ITGA4). shRNA mediated knockdown of one of the identified HOPX regulated genes (integrin alpha 4) in the PR9692 cell line itself showed a marked inhibition of metastasis formation.
Publication Title
Downregulation of HOPX controls metastatic behavior in sarcoma cells and identifies genes associated with metastasis.
Sample Metadata Fields
Cell line
View Samples- Homo sapiens
- 3 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
Most cancer genomics papers to date have focused on aberrations in genomic DNA and protein-coding transcripts. However, around 50% of transcripts have no coding potential and may exist as non-coding RNA. We performed RNA-seq in BRAFv600e melanoma skin cancer and on melanocytes over-expressing oncogenic BRAF to catalog transcriptome remodeling. We discovered that BRAF regulates expression of 1027 protein coding transcripts, 39 annotated lncRNAs and 70 novel transcripts. Many of the novel transcripts are lncRNAs. We used an indepenedent dataset to interrogate our novel transcripts and found that the novel lncRNA BANCR is a BRAF-regulated lncRNA recurrently upregulated in melanoma. Knockdown of BANCR impairs melanoma cell migration.
Publication Title
BRAFV600E remodels the melanocyte transcriptome and induces BANCR to regulate melanoma cell migration.
Sample Metadata Fields
Cell line
View Samples- Saccharomyces cerevisiae
- 127 Downloadable Samples
- Affymetrix Yeast Genome 2.0 Array (yeast2)
Description
Yeast cell cycle transcript dynamics in three S. cerevisiae strains grown at 30 degrees Celsius: cdc20 GALL-CDC20 (persistent mitotic CDK activity; CDK on), cdc8-ts (DNA replication checkpoint), GAL-cse4-353 (spindle assembly checkpoint), cdc8-ts cdc20 (DNA replication checkpoint, CDK on), and cdc8-ts cdc20, rad53-1 (DNA replication checkpoint without Rad53 activity, CDK on) in a BF264-15DU background. We compared transcript levels of genes previously shown to be periodically expressed in wild-type cells and in cells lacking all mitotic cyclins (clb1,2,3,4,5,6; CDK off).
Publication Title
Checkpoints couple transcription network oscillator dynamics to cell-cycle progression.
Sample Metadata Fields
No sample metadata fields
View Samples