Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

7 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

RNA-seq, G pallida population D383 batch 1-2A cyst and hatched J2 samples, exposed for 8h, 24h, 48h to 2nM Solanoeclepin A (dissolved in 1% EtOH), potato root diffusate from wild accession PNT 777-2 (diluted to 0,1x with tap water) or tap water with 1% EtOH (spontaneous hatching control)

ABSTRACT: In this experiment we evaluate the transcriptional responses of G pallida D383 1-2A to diverse hatching stimulations by pure Solanoeclepin A or by potato root exudate. We used cysts hydrated for 7 days in tap water for the experiment. Water for hydration was changed every day. After hydration approximately 13mg of cysts (50-100 cysts) were placed over Netwell inserts (Corning) with 74um mesh size. For this experiment we used 5 “technical” replicates, all performed in the same experiment. Worms underwent the treatment at the Laboratory of Nematology (WUR)(Spit lab) and RNA was extracted in the same lab using the Qiagen RNeasy Micro kit. RNA samples were measured by Nanodrop and Qubit and were sent to the Wageningen BioInformatics business unit. (Wageningen, The Netherlands, Dr. Sara Diaz Trivino’s team) on dry ice. Sequencing was performed by the DLO in Wageningen.

INSTRUMENT(S): Illumina NovaSeq 6000

ORGANISM(S): Globodera pallida

SUBMITTER: Andre Bertran

PROVIDER: E-MTAB-11228 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Quantitative proteomics of Phytophthora infestans life stages

Project description:Samples were isolated from six different P. infestans life stages (hyphae, sporangia, zoospores, cysts, germinated cysts and appressoria).

2017-09-26 | PXD002446 | Pride

Gene expression in populations of the potato cyst nematode Globodera pallida in diapause or quiescence following hydration or exposure to tomato root diffusate

Project description:Plant-parasitic nematodes (PPN) need to be adapted to survive in the absence of a suitable host or in hostile environmental conditions. Various forms of developmental arrest (including desiccation, cryopreservation, hatching inhibition and dauer stages) are used by PPN in order to survive these conditions and spread to other areas. Potato cyst nematodes (PCN) (Globodera pallida and G. rostochiensis) are frequently in a dessicated state unhatched nematodes within the egg dispersal unit inside the cyst. Long term survival seems to be associated primarily with species that have a very restricted host range which requires surviving unhatched in the absence of the host for extended periods of time. This paper shows fundamental changes in the response of quiescent and diapaused eggs of G.pallida to hydration and following exposure to tomato root diffusate using microarray gene expression analysis from a broad set of genes. Surprisingly, many unique genes were activated in the population of diapaused eggs. Transport activity was activated in both quiescent and diapaused eggs; however, the transport function genes were very different between them. Hydrated quiescent and diapaused eggs were markedly different indicating differences in adaptation for long term survival.

2016-02-01 | E-MTAB-3824 | biostudies-arrayexpress

COMPARISON OF THE GIARDIA LAMBLIA TROPHOZOITE AND CYST TRANSCRIPTOME

Project description:To investigate the magnitude of the transcriptional changes occurring during the life cycle of Giardia lamblia we compared the transcriptome of trophozoites and cysts. Cysts were found to possess a much smaller transcriptome, both in terms of mRNA diversity and abundance. Genes encoding proteins related to ribosomal functions are highly over-represented. In cysts which have lost infectivity the transcriptome is further depleted. In contrast, exposure of cysts to conditions which promote excystation induced transcription. Six cysts and three trophozoites life cycle stages were analyzed.

2011-11-09 | E-GEOD-25460 | biostudies-arrayexpress

Identifying Hepatocyte Growth Factor dose response functions in Madin-Darby Canine Kidney Epithelial Cells

Project description:Two biological replicates of Madin-Darby Canine Kidney Epithelial Cells grown as 3D cysts in Collagen Type I (7 days old) were exposed to six different concentrations of Hepatocyte Growth Factor (HGF) (0, 1.03, 2.07, 4.15, 8.33 and 16.67 ng/ml). Total RNA was isolated from the cysts after 12 hours of HGF induction. The data submitted here are the raw sequence files of the single read lengths of 50 bp for the 12 samples (2 replicates X 6 conditions) after RNA sequencing experiment using Illumina HiSeq 2000.15

2016-01-17 | E-MTAB-4959 | biostudies-arrayexpress

Expression data from renal cysts of autosomal dominant polycystic kidney disease (ADPKD) patients

Project description:To elucidate the molecular pathways that modulate renal cyst growth in autosomal dominant polycystic kidney disease (ADPKD) Keywords: Disease state analysis We performed global gene profiling on renal cysts of different size (small cysts: less than 1 ml, n=5; medium cysts: between 10-25 ml, n=5; large cysts: greater than 50 ml, n=3) and minimally cystic tissue (MCT, n=5) from five PKD1 polycystic kidneys. Additionally, non-cancerous renal cortical tissue from three nephrectomized kidneys with isolated renal cell carcinoma was used as normal control tissue (n=3). This dataset is part of the TransQST collection.

2009-08-14 | E-GEOD-7869 | biostudies-arrayexpress

Digital gene expression profiling of the Phytophthora sojae transcriptome

Project description:The transcriptome of the oomycete plant pathogen Phytophthora sojae was profiled at 10 different developmental and infection stages based on a 3'-tag digital gene expression (DGE) protocol. More than 90 million clean sequence tags were generated and compared to the P. sojae genome and its 19,027 predicted genes. A total of 14,969 genes were detected, of which 10,044 were deemed reliable because they mapped to unambiguous tags. A comparison of the whole-library genes expression patterns suggested four groups: 1) mycelia and zoosporangia (MY and SP); 2) zoospores and cysts (ZO and CY); 3) germinating cysts (GC); 4) five infection site libraries (IF1.5 to IF24h). The libraries from the different groups showed major transitional shifts in gene expression. From the ten libraries, 722 gene expression pattern clusters were obtained and the top 16 ones, containing more than half of the genes, comprised enriched genes with different functions including protein localization, triphosphate metabolism, signaling process, and non-coding RNA metabolism. An evaluation of the average expression level of 30 pathogenesis related gene families revealed that most were infection induced, but with diverse expression patterns and levels. A web-based server named the Phytophthora Transcriptional Database (PTD) has been established. The five axenically grown stages were mycelia (MY), zoosporangia (SP), zoospores (ZO), cysts (CY), and germinating cysts (GC). The five infection stages, 1.5, 3, 6, 12 and 24 h after inoculation onto susceptible soybean leaf tissues (IF1.5h to IF24h).

2011-09-01 | E-GEOD-29651 | biostudies-arrayexpress

DNA sequencing of Heterodera schachtii IRS (Woensdrecht) population

Project description:In order to polish a long-read genome assembly, short-read illumina data was obtained from Heterodera schachtii cysts (Woensdrecht population from IRS, the Netherlands). Cysts where obtained from infected plant material. Nematodes were cleaned using a sucrose gradient centrifugation step. Thereafter DNA was extracted and used for library preparation and sequencing by Illumina NextSeq500.

2023-11-03 | E-MTAB-13472 | biostudies-arrayexpress

Digital gene expression profiling of the Phytophthora sojae transcriptome

Project description:This experiment contains Phytophthora sojae samples and RNA-seq data from experiment E-GEOD-29561 (https://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-29651/) to understand gene expression during the P. sojae life cycle. The transcriptome of the oomycete plant pathogen Phytophthora sojae was profiled at 5 different developmental stages: mycelia (MY), zoosporangia (SP), zoospores (ZO), cysts (CY) and germinating cysts (GC); based on a 3'-tag digital gene expression (DGE) protocol. More than 90 million clean sequence tags were generated and compared to the P. sojae genome and its 19,027 predicted genes. A total of 14,969 genes were detected, of which 10,044 were deemed reliable because they mapped to unambiguous tags. A web-based server named the Phytophthora Transcriptional Database (PTD) has been established.

2011-09-01 | E-MTAB-4039 | biostudies-arrayexpress

small RNAseq - Plant parasitic cyst nematodes respond to viral infection through siRNA activation

Project description:In this project we sequenced smallRNAs to see how both BCN (H.schachtii) and PCN (G. rostochiensis line 19 and 22) react to different viruses. After adapter removal, small RNA analysis was performed on sequences from 18 to 28 nt in length. Also the smallRNAs are mapped to the reference genomes of the nematodes to look for smallRNAs.

2023-12-25 | E-MTAB-13351 | biostudies-arrayexpress

Proteomic-based research strategy identified laminin subunit alpha 2 as a potential urinary-specific biomarker for the medullary sponge kidney disease

Project description:Medullary sponge kidney (MSK) disease, a rare kidney malformation featuring recurrent renal stones and nephrocalcinosis, continues to be diagnosed using expensive and time-consuming clinical/instrumental tests (mainly urography). Currently, no molecular diagnostic biomarkers are available. To identify such we employed a proteomic-based research strategy utilizing urine from 22 patients with MSK and 22 patients affected by idiopathic calcium nephrolithiasis (ICN) as controls. Notably, two patients with ICN presented cysts. In the discovery phase, the urine of 11 MSK and 10 controls, were randomly selected, processed, and analyzed by mass spectrometry. Subsequently, several statistical algorithms were undertaken to select the most discriminative proteins between the two study groups. ELISA, performed on the entire patients’ cohort, was used to validate the proteomic results. After an initial statistical analysis, 249 and 396 proteins were identified exclusive for ICN and MSK, respectively. A Volcano plot and ROC analysis, performed to restrict the number of MSK-associated proteins, indicated that 328 and 44 proteins, respectively, were specific for MSK. Interestingly, 119 proteins were found to differentiate patients with cysts (all patients with MSK and the two ICN with renal cysts) from ICN without cysts. Eventually, 16 proteins were found to be common to three statistical methods with laminin subunit alpha 2 (LAMA-2) reaching the higher rank by a Support Vector Machine, a binary classification/prediction scheme. ELISA for LAMA-2 validated proteomic results. Thus, using high-throughput technology, our study identified a candidate MSK biomarker possibly employable in future for the early diagnosis of this disease.

2021-05-24 | PXD025744 | Pride

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