Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Comprehensive bulk RNAseq analysis on whole kidneys during regeneration and fibrosis development reveals sustained dysregulation of immune system related pathways during kidney fibrosis

ABSTRACT: In order to identify the transcriptional changes that correlate with kidney regeneration or fibrosis development, we performed a time-course bulk RNA-seq from whole-kidneys at 3, 7, 14, 28 and 42 days after the initial ischemic kidney from two distinct murine models.

INSTRUMENT(S): Illumina HiSeq 4000

ORGANISM(S): Mus musculus

SUBMITTER: Armelle Lafont

PROVIDER: E-MTAB-7957 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:Organic matter recycling in marine systems is largely driven by microbial processes, particularly in the Arctic where primary production and inputs can be temporally offset from upper trophic level consumption. This study followed bacterial dynamics in the chlorophyll maximum of the Bering Strait and sediment-water interface of the Chukchi Sea using metaproteomic and 16S rRNA methods to measure cellular function and taxonomic composition under low and high marine-derived particulate organic matter (POM) treatments at 0°C. Parallel analysis of major organic components (lipids and amino acids) allowed a comparison of microbial-POM interactions. Over the 10 day experimental period, bacteria under both treatments showed rapid community responses and changes in proteomic expression, accompanied by small changes in the concentration and distributions of organic components. In the Bering Strait community, protein translation was an important immediate cellular response under both POM scenarios while specific metabolic processes were more distinct between treatments. For example, under both conditions, evidence for carboxylic acid metabolism increased at day 6 while carbohydrate utilization as an energy source showed unique patterns as the experiments progressed. With POM additions to the Bering Strait community, nitrogen transport and regulation went up, including nitrogen fixation and ammonia assimilation, by day 6. In addition, a number of vitamin enzymatic cofactors were enriched by this day, providing evidence for an increase in C1 metabolism at that time. Low POM conditions stimulated the cycling and synthesis of amino acids, which was not as pronounced under the high POM treatment. In the Chukchi Sea community, nitrate reduction and substrate-specific transporter activity was statistically higher than in the Bering Strait, especially under low POM conditions. Taxonomic inference revealed that a wide range of bacterial classes were associated with the shifting cellular functions, but that Alphaproteobacteria, Gammaproteobacteria and Flavobacteria controlled most of these protein abundances. Activities of all classes were highly variable, with less dominant bacterial groups exhibiting a particularly strong degree of niche separation.

Dataset Information

Comprehensive bulk RNAseq analysis on whole kidneys during regeneration and fibrosis development reveals sustained dysregulation of immune system related pathways during kidney fibrosis

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