Unknown,Transcriptomics,Genomics,Proteomics

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Iso-seq seuqencing of leukemic pooled samples

ABSTRACT: 2 samples have been prepared for ISO-seq sequencing. CD34+ blast cells from 5 MDS patients before 5-AZA treatment (GEO531A16, GEO531A13, GEO531A5, GEO531A11, GEO531A3) were pooled to generate one sample and 2 AML non-treated and 2 CMML non-treated cells (GEO531A2, GEO531A9, GEO531A6, GEO531A7) were pooled for second sample.

INSTRUMENT(S): Sequel

ORGANISM(S): Homo sapiens

SUBMITTER: Anastasiya Kazachenka

PROVIDER: E-MTAB-8195 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:The hop plant, Humulus lupulus L., contains an exceptionally high content of secondary metabolites, the hop iso-Î±-acids, which possess a range of beneficial properties including antiseptic action. Studies performed on the mode of action of hop iso-Î±-acids have hitherto been restricted to lactic acid bacteria. The present study investigates molecular mechanisms of hop iso-Î±-acid resistance in the model eukaryote Saccharomyces cerevisiae. Growth inhibition occurred at concentrations of hop iso-Î±-acids that were an order of magnitude higher than those found with hop-tolerant prokaryotes. Chemostat-based transcriptome analysis and phenotype screening of the S. cerevisiae haploid gene deletion collection were used as complementary methods to screen for genes involved in hop iso-Î±-acids detoxification and tolerance. Further analysis of deletion mutants confirmed that yeast tolerance to hop iso-Î±-acids involves two major processes: active export of iso-Î±-acids across the plasma membrane and active proton pumping into the vacuole by the V-ATPase to enable vacuolar sequestration of iso-Î±-acids. Furthermore, iso-Î±-acids were shown to affect cellular metal homeostasis by acting as strong zinc and iron chelator. Experiment Overall Design: Two complementary genome-wide approaches were employed to investigate cellular responses of S. cerevisiae to hop extracts enriched in iso-Î±-acids. Microarray transcriptome analysis was performed on chemostat cultures of an S. cerevisiae reference strain grown in the presence and absence of iso-Î±-acids. In addition, screening of the nearly complete set of yeast open reading frame (ORF) haploid knock-outs generated by the Saccharomyces Genome Deletion Project (SGDP) (Open Biosystems) identified the mutants with increased hop sensitivity. Subsequently, involvement of selected genes and cellular processes in hop acid sensitivity and tolerance was analyzed by construction and detailed analysis of selected mutant strains.

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Iso-seq seuqencing of leukemic pooled samples

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