Alternative polyadenylation in the anti-bacterial immune response of zebrafish
No associated publication
None
No sample metadata fields
View SamplesThis dataset contains transcription profiles of TOP10 E.coli transformed with 85 rewired network plasmids first described in: Evolvability and hierarchy in rewired bacterial gene networks. Nature 452:840-5 (2008). The data are described and analysed in an accompanying paper Baumstark et al.,The propagation of perturbations in shuffled bacterial gene networks (Submitted, 2015). 260 raw data microarrays are provided in total, representing biological triplicates (a,b and c; independent colonies grown from the same transformation, under standard growth conditions; LB, 16h). This is done for each of 255 promoter-ORF constructs (e.g. appY-crp, etc.) and 5 control construct microarrays (empty plasmid; Co). Co controls are provided for comparison, to show the relative effect of the rewiring genetic perturbation. The final processed data compares the number of perturbed genes, comparing between the average expression values of each rewired construct and Co. Methods: The 85 rewiring plasmids (Isalan et al, 2008) were transformed into E. coli TOP10 cells and grown under standardised conditions: bacteria were freshly plated onto LB Agar plates (with 100 μg/ml Ampicillin and 50 μg/ml Streptomycin) and incubated overnight at 37oC to form colonies. Single colonies (<3 days old) were used to inoculate 2 ml of LB in 14 ml culture tubes, containing 100 μg/ml Ampicillin and 50 μg/ml Streptomycin. Constructs were grown for 16h at 37oC, at 220 rpm in an orbital shaker. 10 μg of extracted total bacterial RNA (integrity number > 7.0) was used with Affymetrix GeneChip E. coli Genome 2.0 Arrays. Key to names: RAW DATA samples 1-260 _Co_1a.CEL = Control Co, colony a _Co_1b.CEL = Control Co, colony b etc. appY_O_30a.CEL = appY-promoter only, colony a appY_O_30b.CEL = appY-promoter only, colony b etc. appY_crp_34a.CEL = rewired construct, appY-promoter expressing crp ORF, colony a appY_crp_34b.CEL = rewired construct, appY-promoter expressing crp ORF, colony b appY_crp_34b.CEL = rewired construct, appY-promoter expressing crp ORF, colony c etc. PROCESSED DATA sample 261: probe_set_expression_value_norm_all - normalised data for all samples, for all E. coli K12 genes sample 262: probe_set_expression_value_norm_MG1655 - normalised data for all samples, for E. coli MG1655 subset of genes
The propagation of perturbations in shuffled bacterial gene networks
None
No sample metadata fields
View SamplesStudies in human innate lymphoid cell (ILC) development are important in understanding the pathophysiology of immune deficiencies and providing insights into the design of immunotherapies for patients with cancer, infection, and autoimmune disease. Currently, it is unclear where and how ILCs develop in humans. The overall goal of our study is to gain a comprehensive understanding of the cellular and molecular components that regulate human ILC development and function in order to best understand how they work in physiological and pathological states.
No associated publication
None
No sample metadata fields
View SamplesCalcium acts as a universal second messenger to regulate gene expression in both developmental processes and responses to environmental stresses. Previous studies showed that a number of stimuli can induce calcium increases in the cytoplasm and nucleus, independently. However, the gene expression network deciphering [Ca2+]cyt and/or [Ca2+]nuc signaling pathway remain obscure.
No associated publication
Specimen part, Treatment
View Samplescompare the transcriptome changes under high ambient temperature
No associated publication
None
Specimen part, Treatment
View SamplesTo delineate the mechanism underlying SRSF1/delta133p53-mediated alterations in vascular smooth muscle cell (VSMC) proliferation, we analyzed the genome-wide gene expression profiles in cultured human aortic smooth muscle cells (HASMCs) with delta133p53-overexpression and Ang II treatment versus GFP controls using RNA-Seq approach.
No associated publication
None
Sex, Specimen part, Treatment
View SamplesThe RNA-seq data was used to study alternative splicing in Arabidopsis
No associated publication
None
Specimen part, Disease
View Sampleshuman Transcriptomehuman Transcriptomehuman Transcriptomehuman Transcriptomehuman Transcriptome
No associated publication
None
Sex, Age, Specimen part
View SamplesThis study revealed the EP impact on gene expression in fruit fly and provided new insight into the mechanisms of this response, which is helpful for understanding EP toxicity to humans.
No associated publication
None
Sex, Specimen part
View SamplesPlant seedlings undergo distinct developmental processes in the dark and in the light. Using an activation-tagging approach, we identified SRS5ox, which overexpresses SHI-RELATED SEQUENCE 5 (SRS5) following induction with estradiol in Arabidopsis thaliana. SRS5 overexpression in SRS5ox seedlings results in a constitutive photomorphogenesis phenotype in the dark. To investigate potential downstream genes of SRS5, the expression levels of genes assayed by RNA-seq in 5-day-old SRS5ox seedlings grown under white light treated with or without estradiol for 2 hours, respectively.
No associated publication
None
Specimen part
View Samples