Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Paragorgia papillata and Chrysogorgia sp. skeletal proteome

ABSTRACT: This project contains raw bone proteome data for Paragorgia papillata and Chrysogorgia sp.

ORGANISM(S): Octocorallia

SUBMITTER: Kuidong Xu

PROVIDER: PXD056993 | iProX | Sat Oct 19 00:00:00 BST 2024

REPOSITORIES: iProX

ACCESS DATA

Json Xml

Publications

The molecular basis of octocoral calcification revealed by genome and skeletal proteome analyses.

Liang Yanshuo Y Xu Kuidong K Li Junyuan J Shi Jingyuan J Wei Jiehong J Zheng Xiaoyu X He Wanying W Zhang Xin X

GigaScience 20250101

The ability of octocorals and stony corals to deposit calcium carbonate (CaCO3) has contributed to their ecological success. Whereas stony corals possess a homogeneous aragonite skeleton, octocorals have developed distinct skeletal structures composed of different CaCO3 polymorphs and a skeletal organic matrix. Nevertheless, the molecular basis of skeletal structure formation in octocorals remains inadequately understood. Here, we sequenced the genomes and skeletal proteomes of two calcite-formi ...[more]

PMID: 40167990

Similar Datasets

Project description:WTCCC2 project Schizophrenia (SP) samples

| EGAD00010000262 | EGA

Proteome Analysis of Actinoplanes sp. SE50/110

Project description:The acarviose metabolite acarbose is an a glucosidase inhibitor produced by Actinoplanes sp. SE50/110. It is medically important because it is used in the treatment of type 2 diabetes. In this work a comprehensive proteome analysis of Actinoplanes sp. SE50/110 was carried out. The associated txt and RAW files were used for two different analyses and publications. While one study focused on a comparative analysis of Actinoplanes sp. SE50/110 to elucidate differences in the proteome cultures that were grown with either maltose or glucose, the other study applied spectral counting and analyzed only the maltose-grown cultures to determine the major proteins and their location in the cell. The txt files for the comparative data are labeled as "heavy_light" and of the spectral counting data as "light". Both datasets were derived from the same RAW files.

2015-10-21 | PXD001497 | Pride

Muscle and Bone marrow SP and MP cells

2004-11-16 | GSE1571 | GEO

GSC RT-PCR amplification of 10 cells (SP & CD8 T cells), single SP cell and single-SP-cell equivalent

Project description:GSM48315-GSM48332: Ten cells from C57Bl/6 male mouse bone marrow (SP or CD8 T cells) were sorted into individual wells of 96-well plates. The mRNA of these cells was amplified by the global single cell RT-PCR method and biotinylated targets were generated after optimal digestion with DNAse I. GSM48333-GSM48344: Single SP cell from C57Bl/6 male mouse bone marrow were sorted into individual wells of 96-well plates. The mRNA of these single cells was amplified by the global single cell RT-PCR method and biotinylated targets were generated after optimal digestion with DNAse I. GSM48345-GSM48349: Forty bone marrow SP cells from C57Bl/6 male mouse bone marrow, Sca-1 positive and Gr-1 negative, gated on the tip of the SP tail, were sorted into 160 microliters of lysis buffer (40 times the amount used for single cells). 4-microliter aliquots (containing the mRNA equivalent to one single cell) were dispensed into individual wells of 96-well plates. The mRNA contained in each aliquot was amplified by the global single cell RT-PCR method and biotinylated targets were generated after optimal digestion with DNAse I. Detection of the microarray hybridization signals was done according to the standard Affymetrix protocol (antibody amplified). Keywords = HSC Keywords = stem cell Keywords = SP Keywords = side population Keywords = CD8 Keywords = lymphocytes Keywords = global single cell RT-PCR Keywords = GSC RT-PCR Keywords: parallel sample

2006-01-02 | GSE2534 | GEO

Phlpp1 regulates endochondral ossification via the chondrocyte phospho-proteome

Project description:Appendicular growth and bone mass acquisition are controlled by a variety of growth factors, hormones, and mechanical forces in a dynamic process called endochondral ossification. Chondrocytes in the growth plate must proliferate and undergo hypertrophy to drive growth plate expansion and lay the template for bone. Pleckstrin homology (PH) domain and leucine rich repeat phosphatase 1 and 2 (Phlpp1 and Phlpp2) are protein phosphatases that regulate intracellular signaling cascades through posttranslational modification of AKT, PKC, and S6K, among others. Phlpp1 controls chondrocyte proliferation and survival and germline deletion of Phlpp1 suppresses bone lengthening. Here, we demonstrate that Phlpp2 does not regulate endochondral ossification. Phlpp2-/- mice are phenotypically indistinguishable from their wildtype (WT) littermates, with similar bone length, bone mass, and growth plate dynamics. By contrast, Phlpp1/2-/- mice are phenotypically indistinguishable from Phlpp1-/- mice. Deletion of Phlpp1 or Phlpp2 had moderate effects on the chondrocyte transcriptome and proteome compared to WT control cells. By contrast, Phlpp1-/- and Phlpp1/2-/- chondrocytes had significantly altered phospho-proteomes compared to WT and Phlpp2-/- chondrocytes. Data integration via multiomics analysis revealed that RAF-MEK-ERK signaling was altered in cells lacking Phlpp1. In conclusion, these data demonstrate that Phlpp1, but not Phlpp2, regulates endochondral ossification via the chondrocyte phospho-proteome.

2024-09-30 | GSE265773 | GEO

Transcription profiling of mouse muscle and bone marrow SP and MP cells

Project description:This study identified gene expression of Side Population (SP) and Main Population (MP) cells, isolated from adult murine skeletal muscle and Bone Marrow. Five different preparations of muscle SP, muscle MP, Bone marrw SP and Bone marrow MP cells were used as replicates. SUBMITTER_CITATION: Liadaki K, Kho AT, Sanoudou D, Schienda J, Flint A, Beggs AH, Kohane IS, Kunkel LM. Side population cells isolated from different tissues share transcriptome signatures and express tissue-specific markers. Exp Cell Res. 2005;303(2):360-74.

2007-10-11 | E-GEOD-1571 | biostudies-arrayexpress

To screen miRNA expression of SP and MP cells in mutiply myeloma by miRNA array

Project description:To better understand the molecular mechanisms of SP cells, we screened the miRNAs expression patterns in the SP compared with the MP cells. MiRCURY™ LNA array analysis of sorted SP and MP cells from two relapsed myeloma patients with more than 70% bone marrow plasma cells were performed.

2015-12-31 | GSE56163 | GEO

Gene expression profile of zebrafish kidney side population (SP) cells

Project description:Side population (SP) cells are identified based on their capacity to efflux of the fluorescent dye Hoechst 33342, and are enriched for hematopoietic stem cells (HSCs) in mammalian bone marrow. We recently demonstrated that SP cells were present in the teleost kidney, the main hematopoietic organ in teleosts, and were enriched for HSCs. In this analysis, to identify the regulated genes in teleost HSCs, gene expression analysis of zebrafish kidney SP cells were performed using the GeneChip Zebrafish Genome Array.

2008-10-10 | GSE12955 | GEO

Transcription profiling and GSC RT-PCR of mouse bone marrow cells SP and CD8 T cells after amplification, single SP cell and single-SP-cell equivalent to examine diversity of single hematopoietic stem cells

2008-06-12 | E-GEOD-2534 | biostudies-arrayexpress

Proteome dynamics of Microbacterium oleivorans sp. A9 in response to uranium

Project description:The project is a proteomic comparison of Microbacterium sp. A9 exposed to 10 µM nitrate uranyl versus control condition without uranyl. Three sampling time points (30 min, 4h and 24h) were analyzed. The proteomics datasets presented here were obtained using a protein database derived from the Microbacterium sp. A9 complete genome.

2022-04-23 | PXD020998 | Pride

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data