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Arabidopsis thaliana
14 Downloadable Samples
Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
Usually starch is nearly depleted at the end of the night. To induce a gradual depletion of carbon, we have analysed the global response of transcripts during an extension of the night, where carbon becomes severely limiting from about four hours onwards.
Publication Title
Global transcript levels respond to small changes of the carbon status during progressive exhaustion of carbohydrates in Arabidopsis rosettes.
Sample Metadata Fields
Specimen part
View Samples- Arabidopsis thaliana
- 21 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
To investigate the response of Arabidopsis thaliana plants to non-freezing, cool temperatures, we subjected four week old plants to various chilling temperatures at defined times during the diurnal cycle to control for diurnal effects on transcription. From the same plants, metabolites and enzyme activities were measured as well. Interestingly a gradual change could be observed over a wide range of temperatures. Some of which could be attributed to the CBF program.
Publication Title
Multilevel genomic analysis of the response of transcripts, enzyme activities and metabolites in Arabidopsis rosettes to a progressive decrease of temperature in the non-freezing range.
Sample Metadata Fields
Specimen part
View Samples- Arabidopsis thaliana
- 17 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
How do the transcript levels of leaf-expressed genes change in a normal day-night cycle? The interest is in genes that are regulated by the circadian clock and the diurnal component (i.e. light, metabolite changes). Plants were grown on soil in a 12/12 h light/dark rythm at 20C day and night. 5 weeks after germination the rosettes of the non-flowering plants were harvested, 15 plants per sample. Plants were harvested at 6 timepoints every 4 hours beginning with the end of the night (still in darkness).
Publication Title
Sugars and circadian regulation make major contributions to the global regulation of diurnal gene expression in Arabidopsis.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 31 Downloadable Samples
Ion Torrent Proton
Description
In this study we demonstrate that the lung mononuclear phagocyte system comprises three interstitial macrophages (IMs), as well as alveolar macrophages (AMs), dendritic cells and few extravascular monocytes. Through cell sorting and RNAseq analysis we were able to identify transcriptional similarities and differences between the three pulmonary IM subtypes, with reference to the more well-characterized alveolar macrophage Overall design: Pulmonary Interstitial and Alveolar macrophages were FACS sorted from the lungs of steady state 8-10 week old B6 mice, in triplicate. Extracted RNA was examined by RNAsequencing. The tar archive GSE94135_jakubzick_2019*tar available at the foot of this page contains the supplementary processed data used for comparisons with data in GSE132911. Data were processed as described in GSE132911.
Publication Title
Three Unique Interstitial Macrophages in the Murine Lung at Steady State.
Sample Metadata Fields
Specimen part, Cell line, Subject
View Samples- Mus musculus
- 18 Downloadable Samples
- Ion Torrent Proton
Description
Macrophages (MF) have been shown to contribute to fibrogenesis, however the underlying mechanisms and specific MF subsets involved remain unclear. Lung MF can be divided into two subsets: Siglec-Fhi resident alveolar MF and CD11bhi MF that primarily arise from immigrating monocytes. RNA-seq analysis was performed to compare these MF subsets during fibrosis. CD11bhi MF, not Siglec-Fhi MF, expressed high levels of pro-fibrotic chemokines and growth factors. Overall design: C56BL/6 WT mice were treated intratracheally with bleomycin. 8 days later, CD64+Mertk+ MF were sorted into Siglec-F(high) and CD11b(high) subsets. SiglecF(high) MF from naïve mice were also sorted. RNA was isolated and RNA-seq was performed to compare MF subsets.
Publication Title
Deletion of c-FLIP from CD11b<sup>hi</sup> Macrophages Prevents Development of Bleomycin-induced Lung Fibrosis.
Sample Metadata Fields
Sex, Age, Specimen part, Cell line, Treatment, Subject
View Samples- Homo sapiens
- 41 Downloadable Samples
- Illumina HumanHT-12 V3.0 expression beadchip
Description
This study explores the impact of lifestyle and environment on gene expression through whole transcriptome profiling of peripheral blood samples in Fijian population (native Melanesians and Indians) living in the rural and urban areas.
Publication Title
Using blood informative transcripts in geographical genomics: impact of lifestyle on gene expression in fijians.
Sample Metadata Fields
Sex, Age, Specimen part, Subject
View Samples- Drosophila melanogaster
- 12 Downloadable Samples
- Affymetrix Drosophila Genome 2.0 Array (drosophila2)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
Functional genomic analysis of the periodic transcriptome in the developing Drosophila wing.
Sample Metadata Fields
Specimen part
View Samples- Drosophila melanogaster
- 12 Downloadable Samples
Affymetrix Drosophila Genome 2.0 Array (drosophila2)
Description
The eukaryotic cell cycle, driven by both transcriptional and post-translational mechanisms, is the central molecular oscillator underlying tissue growth throughout animals. While genome-wide studies have investigated cell cycle-associated transcription in unicellular systems, global patterns of periodic transcription in multicellular tissues remain largely unexplored. Here we define the cell cycle-associated transcriptome of the developing Drosophila wing epithelium and compare it with that of cultured Drosophila S2 cells, revealing a core set of periodic genes as well as a surprising degree of context-specificity in periodic transcription. We further employ RNAi-mediated phenotypic profiling to define functional requirements for over 300 periodic genes, with a focus on those required for cell proliferation in vivo. Finally, we investigate the role of novel genes required for interkinetic nuclear migration. Combined, these findings provide a global perspective on cell cycle control in vivo, and highlight a critical need to understand the context-specific regulation of cell proliferation.
Publication Title
Functional genomic analysis of the periodic transcriptome in the developing Drosophila wing.
Sample Metadata Fields
Specimen part
View Samples- Drosophila melanogaster
- 9 Downloadable Samples
- Illumina HiSeq 2500
Description
The eukaryotic cell cycle, driven by both transcriptional and post-translational mechanisms, is the central molecular oscillator underlying tissue growth throughout animals. While genome-wide studies have investigated cell cycle-associated transcription in unicellular systems, global patterns of periodic transcription in multicellular tissues remain largely unexplored. Here we define the cell cycle-associated transcriptome of the developing Drosophila wing epithelium and compare it with that of cultured Drosophila S2 cells, revealing a core set of periodic genes as well as a surprising degree of context-specificity in periodic transcription. We further employ RNAi-mediated phenotypic profiling to define functional requirements for over 300 periodic genes, with a focus on those required for cell proliferation in vivo. Finally, we investigate the role of novel genes required for interkinetic nuclear migration. Combined, these findings provide a global perspective on cell cycle control in vivo, and highlight a critical need to understand the context-specific regulation of cell proliferation. Two RNAi lines of CR32027, a non-coding RNA gene identified in this study, are examined for transcriptional changes relative to wt. Overall design: Transcriptional profiles of two RNAi knockdowns, CR32027-IR1 and CR32027-IR2, are examined in Drosophila wing pouch relative to OreR wt in triplicate by RNA Seq.
Publication Title
Functional genomic analysis of the periodic transcriptome in the developing Drosophila wing.
Sample Metadata Fields
Subject
View Samples
GSE34512- Homo sapiens
- 6 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
This study employed Affymetrix GeneChips to profile transcriptome of human pulmonary microvascular endothelial cells (HMVEC-L) treated with PBEFsiRNA to gain insight into transcriptional regulations of PBEF on the endothelial function. We isolated and labeled mRNAs from PBEF siRNA transfected HMVEC-L and hybridized them to Affymetrix GeneChip HG-U133 plus 2. Differentially expressed genes and canonical pathways were analyzed. Expressions of selected genes were validated by RT-PCR or western blotting. Several important themes are emerged from this study. First, PBEF induces the upregulation and downregulation of multiple genes in the endothelium. Expression of 373 genes were increased and 64 genes decreased by at least 1.3 fold in the PBEFsiRNA treated group compared to the control group of PBEFscRNA treated HMVEC-L. Second, the microarray results confirmed some previous reports of PBEF mediated gene expressions in some pathways but provided a more complete repertoire of molecules in those pathways. Third, most of affected canonical pathways or differentially expressed genes in PBEF siRNA treated HMVEC-L over their controls have not previously been reported to be PBEF-responsive. Our first transcriptome analysis of human pulmonary microvascular endothelial cells treated with PBEFsiRNA has provided important insights into the transcriptional regulation of gene expression in HMVEC-L cells by PBEF. Further in-depth follow-up analysis of the transcriptional regulation reported in this study may shed light on molecular mechanisms underlying PBEF mediated endothelial functions and dysfunctions in the physiology and the pathogenesis of inflammatory conditions, cancer, diabetes, coronary heart disease and provide new leads of therapeutic targets to those diseases.
Publication Title
Pleiotropic functions of pre-B-cell colony-enhancing factor (PBEF) revealed by transcriptomics of human pulmonary microvascular endothelial cells treated with PBEFsiRNA.
Sample Metadata Fields
Specimen part
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