Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

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_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.

INSTRUMENT(S): Orbitrap Exploris 480

ORGANISM(S): Chelydra Serpentina

TISSUE(S): Liver

SUBMITTER: Nicole Valenzuela

LAB HEAD: Nicole Valenzuela

PROVIDER: PXD048526 | Pride | 2024-01-30

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	05032023_1.msf	Msf
	05032023_1.raw	Raw
	05032023_1_r2.raw	Raw
	05032023_1_r3.raw	Raw
	Supplementary_Data_Mass_spec.xlsx	Xlsx

Items per page:

1 - 5 of 5

Similar Datasets

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_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.

2024-01-30 | PXD048455 | 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

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

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

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

Project description:Tropical theileriosis in a cattle disease of global economic importance, caused by the tick-borne protozoan parasite Theileria annulata. Conventional control strategies are failing to contain the disease and an attractive alternative is the use of pre-existing genetic resistance or tolerance. However, tropical theileriosis tolerant cattle are less productive than some susceptible breeds. To combine resistance and production traits requires an understanding of the mechanisms involved in resistance. Therefore, we have compared the response of monocytes derived from tolerant (Sahiwals, Bos indicus) and susceptible (Holstein-Friesians, B. taurus) cattle to in vitro infection with T. annulata. Over 150 genes exhibited breed-specific differential expression during the course of infection and nearly one third were differentially expressed in resting cells, implying that there are inherent differences between monocytes from the breeds. Fifty sequences currently only match ESTs or are unique to the library used to generate the microarray. The differential expression of a selection of genes was validated by quantitative RT-PCR, e.g. CD9, prion protein and signal-regulatory protein alpha. A large proportion of the differentially expressed genes encode proteins expressed on the plasma membrane or in the extracellular space and cell adhesion was one of the major Gene Ontology biological processes identified. We therefore hypothesise that the breed-specific tolerance of Sahiwal cattle compared to Holstein-Friesians is due to the interaction of infected cells with other immune cells, which influences the immune response generated against T. annulata infection. The BoMP microarray is available from the ARK-Genomics facility (www.ark-genomics.org).

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

microRNA profiling by array of human skin melanoma and microenvironment

Project description:MicroRNAs are small non-coding molecules about 18-24 nucleotides long which can regulate expression of up to 60% of genes in a cell. So they are involved in many cellular processes. It has been demonstrated that miRNAs are involved in pathological processes, in particular in cancer and may be promising targets for differential diagnosis and therapy of cancer. This study is aimed at finding microRNAs involved in the development of melanoma, which could be potential targets for personalized treatment of this disease.

2019-01-01 | E-MTAB-7060 | biostudies-arrayexpress

Molecular characterization of Quebec Cohort of Primary Breast Cancer FFPE Tissues on the Human Cancer Panel

Project description:Analysis of 97 formalin-fixed, paraffin-embedded (FFPE) primary breast tumors using Illumina DASL microarray technology on a Custom Breast Cancer Panel and the Illumina Human Cancer Panel. Molecular markers between the pathology defined subtypes of breast cancer were assessed to hypothesize potential therapeutic targets specific to the subtypes Molecular Characterization of 97 primary breast tumor formalin-fixed, paraffin-embedded (FFPE) specimens including 24 triple negative (TN: ER-, PR-, HER2-), 9 HER2-positive (HER2+: ER-, PR-, HER2+), and 64 hormone receptor-positive (HR+: ER+ and/or PR+). 91 of the 97 specimens were characterized on the Illumina Human Cancer DASL Panel and 86 of 97 specimens were characterized on a custom Breast Cancer DASL Panel, 80 of these specimens were common to both the Human Cancer DASL Panel and the custom Breast Cancer DASL Panel.

2009-10-23 | E-GEOD-17650 | biostudies-arrayexpress