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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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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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2022-05-16 | E-MTAB-11746 | biostudies-arrayexpress

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

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Project description:PIWI-interacting RNAs (piRNAs) guide PIWI proteins to suppress transposable elements in animal gonads. Here we demonstrate that in the mouse embryonic male germline, endonucleolytic cleavage (slicing) of a transcript by cytosolic MILI acts as a trigger to initiate its further 5??3? processing into non-overlapping fragments. These fragments accumulate as new piRNAs within the nuclear PIWI protein MIWI2. We identify Exonuclease domain-containing 1 (EXD1) as a partner of the established MIWI2 piRNA biogenesis factor TDRD12. Although EXD1 homodimers are inactive as a nuclease, it functions as an RNA adapter within a PET (PIWI-EXD1-Tdrd12) complex. Loss of Exd1 impacts biogenesis of MIWI2 piRNAs and displays a reduction in sequences generated by MILI slicing. This results in selective depletion of repeat piRNAs that target active retrotransposons like LINE1, which are de-repressed in the mutant. We propose that PIWI slicing and EXD1 promote coordination of nucleo-cytoplasmic silencing via piRNA biogenesis.

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