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RNA-seq of precision cut liver slice (PCLS) culture before slicing and up to 9 days after slicing, changing media either every day or every 3 days, with insulin

ABSTRACT: This experiment is designed to test the effect of culture time, media change regime, and insulin on liver slices. Samples were taken before slicing and 3, 4, 5, 6, 7, 8, and 9 days after slicing. Samples had media changed either every day or every three days and insulin was included in the media at 20nM concentration.

INSTRUMENT(S): Illumina HiSeq 2500

ORGANISM(S): Salmo salar

SUBMITTER: Thomas Harvey

PROVIDER: E-MTAB-7367 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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RNA-seq of precision cut liver slice (PCLS) culture before slicing and up to nine days after slicing

Project description:The purpose of this experiment is to test the effect of culture time and on liver slices. We generated liver slices from saltwater-stage Atlantic salmon and cultured them over a period of nine days. Samples were taken before slicing and 1, 3, 4, 5, 6, 7, 8, and 9 days after slicing. After three days, half of the samples were treated with alpha-linolenic acid (ALA) complexed with methyl-beta cyclodextrin (BCD) and the rest received a control treatment of empty BCD.

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RNA-seq of precision cut liver slice (PCLS) culture before slicing and up to nine days after slicing

Project description:RNA-seq of precision cut liver slice (PCLS) culture before slicing and up to nine days after slicing

| PRJEB29531 | ENA

RNA-seq of precision cut liver slice (PCLS) culture before slicing and up to 9 days after slicing, changing media either every day or every 3 days, with insulin

Project description:RNA-seq of precision cut liver slice (PCLS) culture before slicing and up to 9 days after slicing, changing media either every day or every 3 days, with insulin

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Defining the contribution of microRNA-specific slicing Argonautes in animals

Project description:microRNAs regulate gene expression through interaction with an Argonaute protein family member. While some members of this protein family retain an enzymatic activity capable of cleaving RNA molecules complementary to Argonaute-bound small RNAs, the role of the slicing activity in the canonical microRNA pathway is still unclear in animals. To address the importance of slicing Argonautes in animals, we created Caenorhabditis elegans mutant strains carrying catalytically dead endogenous ALG-1 and ALG-2, the only two slicing Argonautes essential for the miRNA pathway in this animal model. We observe that the loss of ALG-1 and ALG-2 slicing activity affects overall animal fitness and causes phenotypes reminiscent of miRNA defects only when grown and maintained at restrictive temperature. Furthermore, the analysis of global miRNA expression show that the catalytic activity of ALG-1 and ALG-2 differentially regulate the level of specific subsets of miRNAs in young adults. We also demonstrate that altering the slicing activity of those miRNA-specific Argonautes does not result in any defect in the production of canonical miRNAs. Together, these data support that the slicing activity of miRNA-specific Argonautes functions to maintain levels of a set of miRNAs for optimal viability and fitness in animals particularly exposed to specific growing conditions.

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In vivo PIWI slicing in mouse testes deviates from rules established in vitro

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RNA-directed DNA methylation involves co-transcriptional small RNA-guided slicing of Pol V transcripts in Arabidopsis.

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Cryo-slicing BN-MS of rat brain mitochondrial proteins

Project description:Blue-native gel electrophoresis (BN) is a powerful method for protein separation. Combined with liquid chromatography-tandem mass spectrometry (LC-MS/MS) it enables large-scale identification of protein complexes and their subunits. Current BN-MS approaches, however, are limited in size resolution, comprehensiveness and quantification. Here, we present a new methodology combining defined sub-mm slicing of BN gels by a cryo-microtome with high-performance LC-MS/MS and label-free quantification of proteins. Application of this cryo-slicing BN-MS approach (csBN-MS) to mitochondria from brain demonstrated a high degree of comprehensiveness, quantification accuracy and size resolution. The technique provided abundance-mass profiles for 743 mitochondrial proteins including all canonical subunits of the oxidative respiratory chain assembled into 13 distinct (super)complexes. Moreover, the data revealed COX7R as a constitutive subunit of distinct supercomplexes and identified novel assemblies of porins and TOM proteins. Together, csBN-MS enables quantitative profiling of complexomes with resolution close to the limits of native gel electrophoresis.

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