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Establishment and Characterization of Turtle Liver Organoids Provides a Potential Model to Decode their Unique Adaptations

ABSTRACT: Raw proteomic dataset from liver-derived organoids associated with Zdyrski et al. 2024 Communications Biology article (https://doi.org/10.1038/s42003-024-05818-1) entitled "Establishment and Characterization of Turtle Liver Organoids Provides a Potential Model to Decode their Unique Adaptations". Files 05032023_2.raw, 05032023_2_f2.raw, 05032023_2_f3.raw, ..... , 05032023_5_r3.raw correspond to samples F4-F15 from Chrysemys picta turtles, as described in the text.

INSTRUMENT(S): Orbitrap Exploris 480

ORGANISM(S): Chrysemys Picta

TISSUE(S): Liver

SUBMITTER: Nicole Valenzuela

LAB HEAD: Nicole Valenzuela

PROVIDER: PXD048455 | Pride | 2024-01-30

REPOSITORIES: Pride

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			Action	DRS
	05032023_1.msf	Msf
	05032023_2.raw	Raw
	05032023_2_f2.raw	Raw
	05032023_2_f3.raw	Raw
	05032023_3.raw	Raw

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Establishment and Characterization of Turtle Liver Organoids Provides a Potential Model to Decode their Unique Adaptations

Project description:Raw proteomic dataset from liver-derived organoids associated with Zdyrski et al. 2024 Communications Biology article (https://doi.org/10.1038/s42003-024-05818-1) entitled "Establishment and Characterization of Turtle Liver Organoids Provides a Potential Model to Decode their Unique Adaptations". Files 05032023_1.raw, 05032023_1_r2.raw, and 05032023_1_r3.raw correspond to samples F1-F3 from Chelydra serpentina turtles as described in the text.

2024-01-30 | PXD048526 | Pride

NOVEL ROLE OF FATTY ACID SYNTHASE IN ANGIOGENESIS THROUGH MODULATION OF LYSINE MALONYLATION OF MTOR

Project description:The role of fatty acid synthesis (FAS) in endothelial cells (ECs) remains incompletely characterized. In this project, we found that silencing of fatty acid synthase (FASN) impedes vessel sprouting by reducing EC proliferation. Moreover, loss of FASN in ECs impaired angiogenesis in vivo, and FASN blockade reduced pathological ocular neovascularization. FASN silencing increased malonyl-CoA levels and immunoblotting of EC lysates for malonylated lysine residues (Kmal) revealed that this led to increased levels of protein malonylation. To identify the nature of some of the malonylated proteins we performed a proteomics screen using an anti-Kmal antibody to enrich Kmal peptides from a tryptic digest of EC lysates, and then analyzed Kmal peptides by LC-MS/MS. In proteomics analysis, we identified malonylation of mTOR at lysine 1218, a poorly characterized post-translational modification. Malonylation of mTOR did not compromise the mTORC1 complex stability or lysosomal membrane localization, but reduced the kinase activity of the complex.

2019-07-08 | PXD006503 | Pride

MicroRNA profiling of human breast cancer cell line MCF7 under conditions of hypoxia

Project description:Hypoxia results in the changes in expression of many genes, the majority of which are mediated via the transcriptional activity of the hypoxia inducible factor (HIF) complex. However, other mechanisms of gene regulation by hypoxia are likely and include control of mRNA stability, regulation of mRNA translation and regulation mediated by micrornas. The aim of this study is to identify microRNAs which expression is regulated by hypoxia. We chose the breast cancer line MCF7 for study as we had previously characterised the expression of the components of the HIF system in that cell line and undertaken an extensive study of the gene expression profile in response to hypoxia, a prolyl hydroxylase inhibitor dimethyloxalylglycine and HIF-1a isoform manipulations (Eldvidge. G.P. et al. (2006) JBC, vol. 281, 22, 15215-15226).

2008-03-01 | E-MEXP-1111 | biostudies-arrayexpress

Systematic Discovery of Deeply Conserved Plant Protein Complexes: hemp

Project description:The associated files are mass spec data from mixed-bed ion exchange chromatography fractions. The starting material wasa clarified homogenate of Trader Joe's "Raw Shelled Hemp Seed".

2019-10-28 | PXD012969 | Pride

Transcription profiling of Yersinia enterocolitica RovA- mutant and wild type strains

Project description:Data is also available from http://bugs.sgul.ac.uk/E-BUGS-51

2007-09-06 | E-BUGS-51 | biostudies-arrayexpress

High throughput sequencing of immunoglobulin (Ig) heavy (IgH) and light (IgL) chain repertoires

Project description:We used 454 sequencing to assess the repertoire of B cell subsets from bone marrow, spleen, and small intestinal lamina propria from two mouse strains. We used a RAG2-GFP reporter mouse strain (129Sve background) to isolate CD19+ RAG2+ B lineage cells from bone marrow and small intestinal lamina propria and total splenic B cells. We used 5' RACE to amplify cDNA libraries using primers specific for the mu constant region of IgH and the Ig kappa constant region. We also used this technique to analyze total B cell libraries from Swiss Webster germ-free mice to compare to littermate controls that were cohoused with regular specific pathogen free (SPF) mice for 7 days. Examination of the Ig kappa repertoire and IgH repertoire in RAG2+ bone marrow B lineage cells compared to RAG2+ small intestinal lamina propria B lineage cells or total splenic B cells. There are 8 (Ig kappa) or 4 (IgH) independent experiments comparing repertoires in RAG2-GFP mice. Each experiment in RAG2-GFP+ mice consisted of a pool of 8-12 mice. There are 3 experiments comparing germ-free to colonized mouse total B cell repertoires, each consisting of one mouse per condition.

2013-07-16 | E-GEOD-48870 | biostudies-arrayexpress

Transcription profiling of bovine monocytes stimulated with with interferon-g and lipopolysaccharide for 2 or 16 hours to validate a bovine macrophage specific cDNA microarray

Project description:Background The response of macrophages to danger signals is an important early stage in the immune response. Our understanding of this complex event has been furthered by microarray analysis, which allows the simultaneous investigation of the expression of large numbers of genes. However, the microarray resources available to study these events in livestock animals are limited. Results Here we report the development of a bovine macrophage specific (BoMP) cDNA microarray. The BoMP microarray contains 5026 sequence elements (printed in duplicate) and numerous controls. The majority of the clones incorporated on the microarray were derived from the BoMP cDNA library generated from bovine myeloid cells subjected to various stimuli, including over 900 sequences unique to the library. Additional clones representing immunologically important genes have been included on the BoMP microarray. The microarray was validated by investigating the response of bovine monocytes to stimulation with interferon-g and lipopolysaccharide using amplified RNA. At 2 and 16 hours post stimulation 695 genes exhibited statistically significant differential expression, including; 26 sequences unique to the BoMP library, interleukin 6, prion protein and toll-like receptor 4. Conclusions A 5K cDNA microarray has been successfully developed to investigate gene expression in bovine myeloid cells. The BoMP microarray is available from the ARK-Genomics facility (www.ark-genomics.org).

2006-09-20 | E-MAXD-16 | biostudies-arrayexpress

Transcription profiling of monocytes derived from tolerant (Sahiwals, Bos indicus) and susceptible (Holstein-Friesians, Bos taurus) cattle to in vitro infection with Theileria annulata

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2007-04-26 | E-MAXD-25 | biostudies-arrayexpress

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