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GSE60438
Homo sapiens
125 Downloadable Samples
Illumina HumanWG-6 v3.0 expression beadchip
Description
Genome-wide analysis of decidual transcriptome in pre-eclampsia compared with normotensive controls to find differentially expressed genes/pathways.
Publication Title
Genome-wide transcriptome directed pathway analysis of maternal pre-eclampsia susceptibility genes.
Sample Metadata Fields
Specimen part, Disease stage
View Samples- Mus musculus
- 24 Downloadable Samples
- Affymetrix Mouse Gene 2.1 ST Array (mogene21st)
Description
Analysis of mouse placenta retrieved at day 18.5pc from vitamin D (1,25-dihydroxyvitamin D3) receptor (Vdr) knockout, heterozygous and wild-type mice. Results provide insight into the molecular mechanisms underlying the effect of vitamin D on placental function.
Publication Title
Vitamin D Receptor Gene Ablation in the Conceptus Has Limited Effects on Placental Morphology, Function and Pregnancy Outcome.
Sample Metadata Fields
Specimen part
View Samples- Homo sapiens
- 18 Downloadable Samples
- Illumina HumanHT-12 V4.0 expression beadchip
Description
Reduced or absent cytotrophoblast invasion of the maternal uterine spiral arteries is a common clinical finding in studies of pregnancies complicated by preeclampsia, suggesting that the mechanisms behind invasion of these cells is perturbed. The placenta initially develops in a low oxygen environment of 1-2% oxygen until after the 10th week of pregnancy. During this time oxygen concentration exerts a major influence over trophoblast activity and, in vitro, hypoxia inducible factors are proposed to be one of many key regulators of first trimester trophoblast behaviour. We used a global gene expression microarray approach to identify signalling pathways involved in invasion of the first trimester trophoblast cell line HTR8/SVneo under hypoxic conditions where HIF-1 was active. Additionally, first trimester placental samples from different gestational age groups were labelled with anti HIF-1 and HIF-2 to evaluate whether HIFs are differentially expressed and localised across the period of development characterised by hypoxia (6-8 weeks) and maternal blood perfusion (10-12 weeks). Eighty-eight genes were differentially expressed between cells cultured in 1% oxygen (where HIF-1 was localised to the nucleus) and 5% oxygen (where HIF-1 was cytoplasmic). 65% of the genes were predicted to contain HIF-1:ARNT transcription factor binding sites. Increased nuclear localisation of HIF-1 was seen in extravillous cytotrophoblasts in early first trimester compared with late, while cellular expression of HIF-2 in the villous stroma was higher in late first trimester. While HIFs and their downstream targets are clearly induced in trophoblasts during early placental development, and in vitro hypoxic conditions, the mechanism and pathways by which invasion is increased under hypoxic conditions is not clear from the gene expression profile. Further insight beyond the transcription level is required to fully understand this complex phenomenon.
Publication Title
Hypoxia induced HIF-1/HIF-2 activity alters trophoblast transcriptional regulation and promotes invasion.
Sample Metadata Fields
Cell line, Treatment
View Samples- Homo sapiens
- 98 Downloadable Samples
- Affymetrix Human Exon 1.0 ST Array [transcript (gene) version (huex10st)
Description
Gene expression changes were assessed from the non sun-exposed skin of the lower back of 98 healthy males aged 19-86. We show that contrary to previous thought, genome wide transcriptional activity does not display an exclusively linear correlation with ageing, but rather, in human skin, undergoes a period of significant transient change between 30 and 45 years of age. The identified transient transcriptional changes suggest a period of heightened metabolic activity and cellular damage mediated primarily through the actions of TP53 (tumour protein 53) and TNF (tumour necrosis factor). We also identified a subgroup of the population characterised by increased expression of a large group of hair follicle genes that correlates strongly with a younger age of onset and increasing severity of androgenetic alopecia.
Publication Title
Transcriptome analysis of human ageing in male skin shows mid-life period of variability and central role of NF-κB.
Sample Metadata Fields
Age, Specimen part
View Samples- Arabidopsis thaliana
- 36 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
Stresses that target mitochondrial function lead to altered transcriptional responses for 100-1000s of genes genome wide, and are signalled via retrograde communication pathways within the cell. rao2 mutants contain a mutation in the NAC family transcription factor ANAC017 and cannot induce stress responsive genes (such as the mitochondrial alternative oxidase 1a) in response to mitochondrial dysfunction. We sought to define the global gene network regulated through RAO2 function in response to mitochondrial stress (mimicked through treatment of plants with antimycin A - a specific inhibitor of complex III in the mitochondrial electron transfer chain), and non-specific stress signals such as hydrogen peroxide. We have defined global stress responses that are positively and negatively mediated by RAO2 function, and show that greater than 80% of transcripts that are differentially regulated under H2O2 stress require proper functioning of ANAC017 for a normal stress responses.
Publication Title
A membrane-bound NAC transcription factor, ANAC017, mediates mitochondrial retrograde signaling in Arabidopsis.
Sample Metadata Fields
Treatment
View Samples- Mus musculus
- 23 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
A transcriptomic meta-analysis of over 400 microarrays was undertaken to compare LPC lines against datasets of; muscle and embryonic stem cell lines, embryonic and developed liver (DL), and HCC. Uploaded here, is the array data from seven of the ten LPC lines used. These seven were prepared in our laboratory. The remaining LPC arrays and arrays from other tissues/cells were obtained from the GEO.
Publication Title
A Transcriptomic Signature of Mouse Liver Progenitor Cells.
Sample Metadata Fields
Sex, Specimen part
View Samples- Arabidopsis thaliana
- 24 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
Arabidopsis ATH1 Genome Arrays were used to analyse changes in transcript abundance between Col-0 (wild-type) Arabidopsis seedlings and either single T-DNA insertional KO mutants of LETM1 (At3g59820)(T-DNA lines; SALK_067558C (letm1-1) and SALK_058471 (letm1-2)) or LETM2 (At1g65540) (T-DNA line; SALK_068877 (letm2-1)). Additionally, letm1 and letm2 knock out Arabidopsis lines were crossed to generate double mutants, however a double knock-out of these two genes results in an embryo lethal phenotype. Hemizygous plants were generated that were homozygous knock out for LETM1 and heterozygous knock out for LETM2, and visa versa, termed (letm1(-/-)LETM2(+/-) and (LETM1(+/-)letm2(-/-) respectively. Note that (letm1(-/-)LETM2(+/-) displays a mild developmental defective phenotype in the first 10-14 days of growth, while (LETM1(+/-)letm2(-/-) shows no phenotype. Microarray analysis was carried out on all three single homozygous knock out lines, and also on both combinations of the hemizygous mutation between the two genes, and compared with a wild-type Col-0 control to gain insight into global transcript abundance changes in these mutant lines. Arrays were performed in triplicate for each genotype, from RNA isolated from 3 independent pools of 5-10 Arabidopsis seedlings at 10 days old.
Publication Title
LETM proteins play a role in the accumulation of mitochondrially encoded proteins in Arabidopsis thaliana and AtLETM2 displays parent of origin effects.
Sample Metadata Fields
Age, Specimen part
View Samples- Arabidopsis thaliana
- 14 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
Karrikins promote seed germination in Arabidopsis thaliana. Completion of germination (protrusion of the radicle) is not observed until ~72 h in dormant wildtype seed under these conditions. We used microarrays to examine karrikin-induced transcriptional changes after 24 h of imbibition. Transcriptional changes may indicate events leading to karrikin-induced germination or karrikin-specific markers.
Publication Title
Karrikins enhance light responses during germination and seedling development in Arabidopsis thaliana.
Sample Metadata Fields
Specimen part, Treatment
View Samples- Vitis vinifera
- 12 Downloadable Samples
- Affymetrix Vitis vinifera (Grape) Genome Array (vitisvinifera)
Description
Sulphur is used as a food preservative, especially throughout the table grape and wine industries, <br></br>however there is increasing concern as to the health rises associated with human consumption. <br></br>Thus, we investigated the transcript abundance changes in grapes treated with sulfur dioxide and <br></br>other preservative compounds, compared to control treatments. Export quality, red-skinned ‘Crimson<br></br> Seedless’ grapes (Vitis vinifera L.) were harvested at commercial maturity from one vineyard <br></br>in the Swan Valley region of Western Australia. At least 15 kg grapes per treatment were <br></br>completely immersed in the treatment solution (? 1 min) and allowed to dry on racks before <br></br>being weighed in to 7 x 2 kg lined export cartons, without sulphur pads. Once packed, cartons <br></br>were immediately placed in 2 °C storage for up to 56 days and once cool, commercial <br></br>SO2-generating pads were placed into cartons for SO2 treatment. The salicylic acid (SA,<br></br> 25 mM), methyl jasmonate (MJ, 5mM) and their combination (25 mM SA + 5 mM MJ) were <br></br>dissolved in 0.5 % (v/v) dimethyl sulphoxide (DMSO). A 0.5 % solution of DMSO was used<br></br> as a control treatment. An additional, untreated control for sulphur-treated berries was used.<br></br>Microarrays were performed in duplicate for the 6 treatments, Sulfur dioxide (plus untreated <br></br>control), SA, MJ, and the combined SAMJ treatment (plus DMSO control) on grape berries <br></br>after 21 days of treatment post harvest. The results indcate a large scale re-programing of <br></br>the grape berry transcritpome, similar to that which has been observed for prolonged <br></br>exposure to harsh oxidative stress conditions.
Publication Title
Sulphur dioxide evokes large scale reprogramming of the grape berry transcriptome
Sample Metadata Fields
Specimen part, Compound
View Samples- Homo sapiens
- 12 Downloadable Samples
- Affymetrix Human Gene 2.0 ST Array (hugene20st)
Description
3mm punch biopsies were taken from a healed normotrophic scar and a contralateral matched control site in burn patients with a scar at least 1 year old. Fibroblasts were cultured from explants to passage 2 and RNA was extracted and run on expression arrays to examine differences in scar and control fibroblast gene expression
Publication Title
No associated publication
Sample Metadata Fields
Sex, Age, Specimen part, Subject
View Samples