Project description:A RNA Seq analysis of 7 tissues from 16 week old male knockout mice. A total of 106 IMPC knockout lines were analysed by David West's group at Children's Hospital Oakland Research Institute.
Project description:This is a pilot study from the Knockout Mouse Phenotyping Program (KOMP2). The program provides broad, standardized phenotyping of a genome-wide collection of mouse knockouts generated by the International Knockout Mouse Consortium (IKMC), funded by the NIH, European Union, Wellcome Trust, Canada, and the Texas Enterprise Fund. In this experiment RNAseq was performed to profile expression of coding RNA in the liver, spleen, kidney, abdominal muscle and gonadal adipose tissue of knock out mice (1810027O10Rik knockout, Sik1 knockout, 3110043O21Rik knockout, 3110043O21Rik knockout) compared with wild type controls.
Project description:Maize and rice are the two most economically important grass crops and utilize distinct forms of photosynthesis to fix carbon: C4 and C3 respectively. Relative to C3 photosynthesis, C4 photosynthesis reduces photorespiration and affords higher water and nitrogen use efficiencies under hot arid conditions. To define key innovations in C4 photosynthesis, we profiled metabolites and gene expression along a developing leaf gradient. A novel statistical method was implemented to compare transcriptomes from these two species along a unified leaf developmental gradient and define candidate cis-regulatory elements and transcription factors driving photosynthetic gene expression. We also present comparative primary and secondary metabolic profiles along the gradients that provide new insight into nitrogen and carbon metabolism in C3 and C4 grasses. These resources, including community viewers to access and mine these datasets, will enable the elucidation and engineering of C4 photosynthetic networks to improve the photosynthetic capacity of C3 and C4 grasses. [Maize] Nine day old third leaves of maize were cut into fifteen 1 cm segments; samples were pooled from an average of seven plants per biological replicate and six biological replicates in total were collected on different dates. [Rice] 14 day old third leaves of rice were cut into eleven 2 cm segments, samples were pooled from an average of 15 plants per biological replicate and four replicates in total were collected.
Project description:PeptideRank is an approach that uses a rank-based algorithm for peptide detectability prediction from shotgun proteomics data. The best performance is achieved when it is trained on organism-specific shotgun proteomics datasets. The Drosophila shotgun proteomics data presented here have been used amongst others to train and validate PeptideRank.
Project description:Background: Pyrazinamide (PZA) plays an essential part in the shortened 6-month tuberculosis (TB) treatment course due to its activity against slow-growing, semi-dormant organisms. We tested the paradigm that PZA preferentially targets slow growing cells of Mycobacterium tuberculosis that remain after the initial kill by isoniazid, by observing the response of either slow growing or fast growing bacilli to differing concentrations of PZA. Methods: M. tuberculosis H37Rv was grown in continuous culture at either a constant fast growth rate (Mean Generation Time [MGT] of 23.1 h) or slow growth rate (69.3 h MGT) at a controlled dissolved oxygen tension of 10% and a controlled acidity at pH 6.3 ± 0.1. The cultures were exposed to step-wise increases in the concentration of PZA (25 µg ml-1 to 250 µg ml-1) every 2 MGTs, and bacterial survival was measured. PZA-induced global gene expression was explored for each increase in PZA-concentration, using microarray.
Project description:MaSC, Luminal progenitor enriched subpopulations were isolated from virgin and pregnant mice based on using both surface marker or internal reporter transgene (GFP) expression. (Tiede BJ et al., 2009, PLoS ONE 4(11): e8035. doi:10.1371/journal.pone.0008035), and the transcirptome profiles were determined and compared. Two MaSC differential methods: CD24/CD29 & GFP reporter; two physiolgical condition: virgin vs pregnant; the combination of ((P4, GFPhi) vs (P5, P6, GFPlo)) x (vg vs pg)
Project description:MaSC, luminal progenitor enriched subpopulations and total MECs as well, were isolated from both wild type and ∆Np63 KO heterozygous mouse and the transcriptome profiles were determined and compared. Three populations: P4, P5 and MECs; two genotypes: WT vs ∆Np63 heterozygous.
Project description:Profiling of transcripts specific for cardiomyocytes and non-cardiomyocytes in the mouse heart. Cells were isolated according to: MiRNA-1/133a Clusters Regulate Adrenergic Control of Cardiac Repolarization. Besser J, Malan D, Wystub K, Bachmann A, Wietelmann A, Sasse P, Fleischmann BK, Braun T*, Boettger T*. PLoS One. 2014 Nov 21;9(11):e113449. doi: 10.1371/journal.pone.0113449. PMID: 25415383
Project description:During its life cycle, the helminth parasite Schistosoma mansoni uses the freshwater snail Biomphalaria glabrata as an intermediate host to reproduce asexually generating cercariae for infection of the human definitive host. Following invasion of the snail, the parasite develops from a miracidium to a mother sporocyst and releases excretory secretory products (ESPs) that likely influence the outcome of host infection. To better understand molecular interactions between these ESPs and the host snail defence system, we determined gene expression profiles of haemocytes from S. mansoni resistant or -susceptible strains of B. glabrata exposed in vitro to S. mansoni ESPs (20ug/ml) for 1 h, using a 5K B. glabrata cDNA microarray.