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SRP132308
Drosophila melanogaster
12 Downloadable Samples
Illumina HiSeq 2000
Description
Purpose: Investigating the role of Drosophila G9a in oxidative stress responses. Methods: Flies were collected after eclosion and allowed to recover from CO2 exposure for 5 days prior to paraquat exposure. Paraquat (Methyl viologen dichloride hydrate 98 %; Sigma 856177) was mixed into the flyfood at 40 °C to a final concentration of 50 mM. For OS induction, 5-9 day old flies were transferred to paraquat containing food and incubated at 25 °C and 70 % humidity. At each time point, flies were flash frozen in liquid nitrogen followed by vortexing and filtering through a series of sieves to isolate heads from other body parts. 200 fly heads per sample were used for RNA extraction using QIAGEN lipid mini tissue kit. The TruSeq RNA Sample Preparation Kit v2 (Illumina) was used to prepare adapter ligated PCR fragments for sequencing. PCR was used to selectively enrich the fragments containing the adapters. The PCR fragments were validated using Agilent 2200 TapeStation. Single indexed samples were multiplexed and sequenced on an Illumina HiSeq 2000 sequencing system (Illumina) in single-end mode with a read length of 35 bp. Quality of sequenced reads was assessed with FastQC. The RNAseq experiments were conducted on two biological duplicates for each condition. Sequenced reads were aligned with Burrows-Wheeler algorithm (BWA) (Li & Durbin, 2010) to the Drosophila reference genome (BDGP.5, http://www.fruitfly.org/) and per gene read counts were generated with HTSeq count (Anders et al, 2015). 25–30 million reads with high quality alignment were obtained for each sample and used for differential expression analysis. DESeq (Anders & Huber, 2010) was used to obtain library size-normalized read counts and to calculate differential expression of genes in 4 pairwise comparisons: 0 h versus 6 h and 0 h versus 12 h after OS in both G9a mutants and controls (fold change =1.5, adjusted p-value= 0.05, Benjamini-Hochberg). Results: We found 2731 genes to be differential expressed in at least one of the four pairwise comparisons. The largest group of differentially expressed (DE) genes are highly augmented upon OS induction in the G9a mutant (41.7 % of all DE genes). The second largest group of DE genes (23.9 % of all DE genes) were more downregulated in G9a mutant in response to OS. Genes that are over-activated in G9a mutants are predominantly involved in OS response and OS mediated damage, whereas genes that are downregulated in G9a mutants are involved in energy metabolism. Conclusions: Our data suggest that G9a provides an epigenetic mechanism that safeguards an appropriate transcriptional response to OS and preserves immediately available energy, thereby acting as a critical regulatory hub between the transcriptional and physiological responses to oxidative stress. Overall design: fly-head mRNA libraries of 5-9 days old male G9aDD1 mutant and control during 0, 6 and 12 hours of paraquat oxidative stress exposure were sequenced in duplicate on Hi-seq 2000.
Publication Title
The histone methyltransferase G9a regulates tolerance to oxidative stress-induced energy consumption.
Sample Metadata Fields
Specimen part, Treatment, Subject
View Samples- Homo sapiens
- 98 Downloadable Samples
Illumina HumanHT-12 V4.0 expression beadchip, Illumina HumanWG-6 v3.0 expression beadchip
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
Pretreatment microRNA Expression Impacting on Epithelial-to-Mesenchymal Transition Predicts Intrinsic Radiosensitivity in Head and Neck Cancer Cell Lines and Patients.
Sample Metadata Fields
Sex, Specimen part, Cell line
View Samples- Homo sapiens
- 96 Downloadable Samples
Illumina HumanWG-6 v3.0 expression beadchip
Description
Purpose: Predominant causes of head and neck cancer recurrence after radiotherapy are rapid repopulation, hypoxia, fraction of cancer stem cells and intrinsic radioresistance. Currently, intrinsic radioresistance can only be assessed by ex-vivo colony assays. Besides being time-consuming, colony assays do not identify causes of intrinsic resistance. We aimed to identify a biomarker for intrinsic radioresistance to be used before start of treatment and to reveal biological processes that could be targeted to overcome intrinsic resistance.
Publication Title
Pretreatment microRNA Expression Impacting on Epithelial-to-Mesenchymal Transition Predicts Intrinsic Radiosensitivity in Head and Neck Cancer Cell Lines and Patients.
Sample Metadata Fields
Specimen part, Cell line
View Samples- Homo sapiens
- 2 Downloadable Samples
- Illumina HumanWG-6 v3.0 expression beadchip
Description
Purpose: Predominant causes of head and neck cancer recurrence after radiotherapy are rapid repopulation, hypoxia, fraction of cancer stem cells and intrinsic radioresistance. Currently, intrinsic radioresistance can only be assessed by ex-vivo colony assays. Besides being time-consuming, colony assays do not identify causes of intrinsic resistance. We aimed to identify a biomarker for intrinsic radioresistance to be used before start of treatment and to reveal biological processes that could be targeted to overcome intrinsic resistance.
Publication Title
Pretreatment microRNA Expression Impacting on Epithelial-to-Mesenchymal Transition Predicts Intrinsic Radiosensitivity in Head and Neck Cancer Cell Lines and Patients.
Sample Metadata Fields
Specimen part
View Samples- Homo sapiens
- 72 Downloadable Samples
- Affymetrix Human Gene 1.0 ST Array (hugene10st)
Description
Systemic inflammation like in sepsis is still lacking specific diagnostic markers and effective therapeutics. The first line of defense against intruding pathogens and endogenous damage signals is pattern recognition by e.g., complement and Toll-like receptors (TLR). Combined inhibition of a key complement component (C3 and C5) and TLR-co-receptor CD14 has been shown to attenuate certain systemic inflammatory responses. Using DNA microarray and gene annotation analyses, we aimed to decipher the effect of combined inhibition of C3 and CD14 on the transcriptional response to bacterial challenge in human whole blood. Importantly, combined inhibition reversed the transcriptional changes of 70% of the 2335 genes which significantly responded to heat-inactivated Escherichia coli by on average 80%. Single inhibition was less efficient (p<0.001) but revealed a suppressive effect of C3 on 21% of the responding genes which was partially counteracted by CD14. Furthermore, CD14 dependency of the Escherichia coli-induced response was increased in C5-deficient compared to C5-sufficient blood. The observed crucial distinct and synergistic roles for complement and CD14 on the transcriptional level correspond to their broad impact on the inflammatory response in human blood, and their combined inhibition may become inevitable in the early treatment of acute systemic inflammation.
Publication Title
CD14 and complement crosstalk and largely mediate the transcriptional response to Escherichia coli in human whole blood as revealed by DNA microarray.
Sample Metadata Fields
Specimen part
View Samples- Mus musculus
- 7 Downloadable Samples
- Affymetrix Mouse Gene 1.0 ST Array (mogene10st)
Description
We have isolated cells from the B16F10 melanoma cell line which express the vascular-selective marker PECAM1
Publication Title
Vascular channels formed by subpopulations of PECAM1+ melanoma cells.
Sample Metadata Fields
Cell line
View Samples- Homo sapiens
- 160 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
POU2AF1 Functions in the Human Airway Epithelium To Regulate Expression of Host Defense Genes.
Sample Metadata Fields
Specimen part, Cell line, Race, Time
View Samples- Homo sapiens
- 160 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
In the process of seeking novel lung host defense regulators by analyzing genome-wide RNA sequence data from normal human airway epithelium, we detected expression of POU2AF1, a known transcription co-factor previously thought to be expressed only in lymphocytes. Lymphocyte contamination of human airway epithelial samples obtained by bronchoscopy and brushing was excluded by immunohistochemistry staining, the observation of up-regulation of POU2AF1 in purified airway basal stem/progenitor cells undergoing differentiation and analysis of differentiating single basal cell clones. Lentivirus-mediated up-regulation of POU2AF1 in airway basal cells induced up-regulation of host defense genes, including MX1, IFIT3, IFITM and known POU2AF1 downstream genes HLA-DRA, ID2, ID3, IL6, BCL6. Interestingly, expression of these genes paralleled changes of POU2AF1 expression during airway epithelium differentiation in vitro, suggesting POU2AF1 helps to maintain a "host defense tone" even in pathogen-free condition. Cigarette smoke, a known risk factor for airway infection, suppressed POU2AF1 expression both in vivo in humans and in vitro in human airway epithelial cultures, accompanied by deregulation of POU2AF1 downstream genes. Finally, enhancing POU2AF1 expression in human airway epithelium attenuated the suppression of host defense genes by smoking. Together, these findings suggest a novel function of POU2AF1 as a potential regulator of host defense genes in the human airway epithelium.
Publication Title
POU2AF1 Functions in the Human Airway Epithelium To Regulate Expression of Host Defense Genes.
Sample Metadata Fields
Specimen part, Race, Time
View Samples- Mus musculus
- 2 Downloadable Samples
- Affymetrix Mouse Gene 1.0 ST Array (mogene10st)
Description
Adipose tissue iNKT cells have different functions than iNKT cells in the blood and other organs.
Publication Title
Regulatory iNKT cells lack expression of the transcription factor PLZF and control the homeostasis of T(reg) cells and macrophages in adipose tissue.
Sample Metadata Fields
Age, Specimen part
View Samples- Mus musculus
- 18 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
The objective of this study is to assess the effects of the Serum Response Factor deletion on the cardiac gene expression program at different time points after the deletion (day 8 and day 25) and to compare the response of SRF-deficient heart and control heart to phenylephrine, an alpha-adrenergic agonist triggering cardiac hypertrophy.
Publication Title
Nicotinamide Riboside Preserves Cardiac Function in a Mouse Model of Dilated Cardiomyopathy.
Sample Metadata Fields
Sex
View Samples