Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

A seed-like proteome in oil-rich tubers

ABSTRACT: Fresh tubers were harvested from purple nutsedge and dried.

INSTRUMENT(S): Q Exactive HF

ORGANISM(S): Cyperus Rotundus

TISSUE(S): Tuber

SUBMITTER: Till Ischebeck

LAB HEAD: Till Ischebeck

PROVIDER: PXD035931 | Pride | 2022-10-31

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Similar Datasets

A seed-like proteome in oil-rich tubers

Project description:There are numerous examples in plants, where certain organs or developmental stages are desiccation tolerant and can withstand extended periods of severe water loss. One prime example are seeds and pollen of many spermatophytes. However, in some plants, also vegetative organs can be desiccation tolerant as for example the tubers of yellow nutsedge (Cyperus esculentus) that also store larger amounts of lipids similar to seeds. Interestingly, the closest relative purple nutsedge (Cyperus rotundus) generates tubers that do not accumulate oil and are not desiccation tolerant. We generated nanoLC-MS/MS-based proteomes of yellow nutsedge in five replicates of four stages of tuber development and compared them to the proteomes of roots and leaves, yielding 2257 distinct protein groups. Our data reveal a striking upregulation of hallmark proteins of seeds in the tubers. A deeper comparison to the tuber proteome of the closest relative purple nutsedge (Cyperus rotundus) and a previously published proteome of Arabidopsis seeds and seedlings indicates that indeed a seed-like proteome was found in yellow but not purple nutsedge. This was further supported by an analysis of the proteome of a lipid-droplet enriched fraction of yellow nutsedge, which also displayed seed-like characteristics. One reason for the differences between the two nutsedge species might be the expression of certain transcription factors homolog to ABSCISIC ACID INSENSITIVE3, WRINKLED1 and LEAFY COTYLEDON1 that drive gene expression in Arabidopsis seed embryos.

2022-10-31 | PXD031123 | Pride

RNA seq of human fibroblasts treated with Rocuronium bromide

Project description:Cancer associated fibroblasts (CAFs) as the main stromal cells in tumor microenvironment can provide metabolic links with tumor cells through metabolic derivatives such as cytokines released, creating a favorable metabolic microenvironment for tumor progression. Recent in vitro and in vivo studies have discovered that anesthetics can affect tumor malignancy. However, the mechanism is unknown, and the total-body dosage and short-term treatment duration of anesthetic drugs are still far from tumor treatment. Now, our study focuses on the effect of rocuronium bromide (RB) on CAFs. In order to restore the true effects of CAFs by RB, we studied the global transcriptomic signatures of human fibroblasts derived from different tissues (skin HS-27; lung TIG-1; dermal CRL-7815) by 160 μg/mL RB to find the target genes responding to RB.

2022-05-22 | E-MTAB-11728 | biostudies-arrayexpress

YTHDF3 improves translation initiation of mRNAs with N6-methyladenosine methylation at 5’ untranslated region by facilitating eIF2AK2 recruitment in oxaliplatin-resistant colorectal cancer - RNA-seq cell line comparison

2022-02-04 | E-MTAB-11322 | biostudies-arrayexpress

The analysis of transcriptional profiles of cybrid cells harbouring two pathogenic mtDNA variants associated with Leigh syndrome

Project description:The analysis of transcriptional profiles of cybrid cells harbouring two pathogenic mtDNA variants associated with Leigh syndrome i.e., m.9185T>C in the mt-ATP6 gene and m.13513G>A in the mt-ND5 gene, in comparison to cybrid cells harbouring control mtDNA haplogroups or the wt m.13513G variant.

2023-04-01 | E-MTAB-11035 | biostudies-arrayexpress

Genome-wide binding signature of Signal transducer and activator of transcription (STAT) family in colorectal cancer HCT 116 cell

Project description:The excessive and continuous activated Janus kinase/signal transducer and activator of transcription (JAK/STAT) pathway leads to the proliferation and migration of malignant cells resulting in the occurrence and development of almost all of cancers. The defined gene sets specifically activated by different STAT proteins are relied on their genomic accessibility by the interplay of certain STAT proteins with other potential cofactors. However, we have no clue about the status of human activated STAT dimers in the nucleus, as well as the intercrossing modules of synergic, supplementary or competitive relationship among each other in colorectal cancer. In current study, chromatin immunoprecipitation sequencing (ChIP-seq) was conducted to explore the genome-scale binding signatures of STAT1, STAT2, STAT3, STAT5A/B and STAT6 in human HCT-116 CRC cells. Moreover, STAT3 binding on genomic DNA was also investigated in HCT116 cells with NR5A2 knockdown.

2021-11-08 | E-MTAB-11113 | biostudies-arrayexpress

Paradoxical drug sensitization of lung cancer cells by stromal fibroblast-secreted IGF-binding proteins: Secretomics

Project description:Cancer-associated fibroblasts (CAFs) are an integral part of the tumor microenvironment often linked to drug resistance. Here, we report that CAFs, but not normal fibroblasts, can promote either resistance or unexpected drug sensitization of different lung cancer cells. Using unbiased secretomics, transcriptomics and tyrosine phosphoproteomics, we observed differential expression of several IGF1R signaling components, such as IGF-binding proteins and IGF1/2, and downstream signaling effects on cancer cells by fibroblasts. IGF1/2 treatment or IGFBP5 silencing in CAFs reversed, while addition of exogenous IGFBPs or pharmacological IGF1R inhibitors phenocopied the sensitizing effects. Combining IGF1R and EGFR inhibitors synergized in 2D and 3D models of different drug-resistant and naïve EGFR-mutant lung cancer cells and decreased tumor growth in vivo. These results suggest that multiple resistance mechanisms coexist within the same cancer cells, that CAFs context-dependently cause drug resistance or sensitization, and that understanding both of these differential mechanisms leads to improved therapeutic approaches.

2023-03-11 | PXD023626 | Pride

Project description:Oxaliplatin as a first-line drug frequently causes the chemo-resistance on colorectal cancer (CRC). N6-methyladenosine (m6A) methylation has been largely acknowledged in multiple biological functions. However, the molecular mechanisms underlying the m6A methylation in modulating anticancer drug resistance in CRC are still obscure. In present study, RIP-seq was conducted to investigate the occupancy of N6-methyladenosine RNA binding protein 3 (YTHDF3) served as “readers” that can recognize m6A modification site in HCT116 cells with oxaliplatin resistance (HCT116R). Then, YTHDF3 was knockdown by siRNA in HCT116 cells with oxaliplatin resistance, and RIP-seq was further conducted to investigate m6A methylation of HCT116, HCT116R and HCT116R cells with YTHDF3 knockdown.

2022-02-04 | E-MTAB-11321 | biostudies-arrayexpress

RNA-Seq of monoclonal cell lines after CRISPR/Cas9-mediated editing of box C/D snoRNA genes (SNORDs)

Project description:In this study monoclonal cell lines carrying mutations in snoRNA genes (SNORD74, SNORD75, SNORD77, SNORD80) were obtained. Next, whole transcriptome analysis of obtained cell lines was performed on an Illumina NextSeq 500 platform. RNA-seq libraries was constructed on PolyA mRNA-enriched fraction. The comparison of the expression levels of genes and transcripts in RNA-Seq experiments was carried out using CuffDiff tool. Mutations in SNORD75 in the obtained monoclonal cell line were shown to result in aberrant splicing of Gas5.

2019-10-14 | E-MTAB-8269 | biostudies-arrayexpress

Transcriptomic characterization of the human cell cycle in individual unsynchronized cells

Project description:Here, we profiled transcription across the cell cycle in single human myxoid liposarcoma cells, without prior synchronization. Flourescence-activated cell sorting was used to infer G1, S or G2/M cell cycle stages after staining cells for DNA content. Single-cell RNA-sequencing was performed according to the Smart-seq2 protocol.

2017-11-09 | E-MTAB-6142 | biostudies-arrayexpress

The transcriptome of TRPV1-positive sensory neurons revealed by subgroup-elimination transcriptomics

Project description:We developed an approach to rapidly eliminate the subgroup of sensory neurons expressing the heat-gated cation channel TRPV1 from dissociated rat sensory ganglia using agonist treatment followed by density centrifugation. To identify transcripts predomintly expressed in TRPV1-positive neurons, we compared the transcriptome of all cells within sensory ganglia versus all cells without TRPV1 expressing neurons using RNA-Seq. Four replicate experiments with RNA from DRG neurons of one rat per experiment were performed. Dissociated neurons were split up in three parts, treated with solvent DMSO (0.1%), casaicin (10 µM), or RTX (100 nM) for 30 min followed by gradient centrifugation. RNA was extracted from the remaining pellet containing either all cells or all cells without TRPV1-positive neurons.

2015-05-12 | E-GEOD-59727 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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