Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Comparison between two different Pinus pinaster provenances (RNA-Seq)

ABSTRACT: The transcriptome of needles from plants propagated by cuttings and cultured in the same conditions at SERIDAâ??s greenhouse at Villaviciosa (Asturias, Spain) were analyzed. The cuttings are from two different provenances of Pinus pinaster; Leiria (Portugal) and Tamrabta (Morocco). Their transcriptomes were analyzed using high throughput sequencing 4 samples

ORGANISM(S): Pinus pinaster

SUBMITTER: Rafael CaÃ±as

PROVIDER: E-GEOD-61923 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Comparison between two different Pinus pinaster provenances

Project description:The transcriptome of needles from plants propagated by cuttings and cultured in the same condictions at SERIDAâs greenhouse at Villaviciosa (Asturias, Spain) were analyzed. The cuttings are from two different provenances of Pinus pinaster; Leiria (Portugal) and Tamrabta (Morocco). Their transcriptomes were analyzed using one color microarrays.

2015-11-04 | E-GEOD-61801 | biostudies-arrayexpress

Transcriptional profiling of shoots and roots in japonica and indica rice seedlings under salt stress and recovery stage

Project description:Rice seedlings at 3-leaf stage were used for expression analysis in control and salt stressed (incloudling salt treatment for 3, 24hrs and recovery from cold stress for 24hrs) samples. Samples of shoots and roots from biological replicates of both genotypes were generated and the expression profiles were determined using Phalanx Rice OneArrayï¼ v1. Control and treated biological replicates of salt-tolerant cultivar TNG67 (japonica) and salt-sensitive cultivar TCN1 (indica) were analyzed

2016-06-30 | E-GEOD-76613 | biostudies-arrayexpress

Gene expression analysis during adventitious root formation in petunia cuttings

Project description:In order to identify genes specifically induced during various developmental stages of Adventitious Root (AR) formation (described in Ahkami et al. 2009) in leafy cuttings of Petunia hybrida (line W115) and to describe the series of physiological processes during adventitious rooting, a microarray-based transcriptome analysis in the stem base of the cuttings was conducted. The microarray was described by Breuillin et al. (2010) and included a normalized cDNA library from different time points after taking the cuttings from mother plant. Because physiological processes and molecular changes specifically involved in AR formation were considered as of major interest, rather than those associated with wound responses, a filtration approach was chosen to eliminate primarily wound-responsive genes. This study is mainly focused on changes in transcript abundances of genes related to specific metabolic pathways or cellular events including primary metabolism, membrane transport, cell division or signalling during various phases of AR formation. The overall design of the custom microarray used in this study is described in Breuillin et al. (2010). In brief, a database of 24,816 unigene sequences (including 4,700 ESTs from P. hybrida cutting base and all public available P. hybrida and P. axillaris sequences) was used for construction of a custom microarray.

2014-05-17 | E-GEOD-57752 | biostudies-arrayexpress

Small RNA-seq on a time series of potato infected with Globodera pallida

Project description:We explored the sex determination of Globodera pallida. To do so, we grew cuttings of the potato cultivar Desiree on Gamborg B5 medium supplemented with either 1.5 g/L or 20 g/L sucrose. 14-day-old cuttings were inoculated with 100 G. pallida E400 Rookmaker juveniles. Infected root tissue was harvested at 1, 3, 6, and 9 dpi. Also, a subsample of the ppJ2 was kept for each batch. The experiment contains four time-separated batches. Small RNA sequencing was performed by BGI Hong Kong.

2025-11-05 | E-MTAB-15069 | biostudies-arrayexpress

Transcription profiling by array of tobacco (Nicotiana tabacum) plants in response to sulfur deficiency

Project description:The experiment was aimed at identification of genes whose expression is up- or down-regulated in tobacco plants in response to sulfur (S) deficiency. Comparison of response to S deficit of LA Burley 21 line and AB3 line (overexpressing UP9C in antisense orientation) was done to clarify the function of LSU/UP9 family genes.

2013-02-14 | E-MEXP-3699 | biostudies-arrayexpress

Time-series RNA-seq on potato root tissue infected by two populations of Globodera pallida

Project description:In this experiment we follow the infection of potato by Globodera pallida populations AMPOP02 and Rookmaker. The goal of the experiment was twofold: (i) to follow the expression of effectors in the nematode, (ii) to follow the transcriptional response of the potato plant. In this experiment, we inoculated 14 day old potato cuttings of the variety Seresta with AMPOP02, Rookmaker, or a mock-infection. Root tissue was harvested at 1, 3, 6 and 9 days post infection. Also, a subsample of the pre-parasitic juveniles used as the inoculum was kept for each batch. The experiment contains four time-separated batches. RNA extraction was done in Wageningen. Sequencing was performed by BGI Hong Kong.

2025-08-05 | E-MTAB-15312 | biostudies-arrayexpress

RNA-seq studies using wheat PHYTOCHROME B and PHYTOCHROME C mutants reveal shared and specific functions in the regulation of flowering and shade-avoidance pathways

Project description:The phytochromes (PHYs) are a family of photoreceptors which absorb light of red and far-red wavelengths to modulate developmental responses in photosynthetic organisms. We developed knockout mutants of PHYB and PHYC in wheat and performed replicated RNA-seq studies to analyze and compare the regulons of each phytochrome under long day photoperiods. Illumina Truseq v2 RNA-seq libraries were constructed from four biological replicates of phyBnull mutants and their wild-type sister lines and of phyCnull mutants and their wild-type sister lines. Subsequently, the entire experiment was replicated. Reads were mapped to the draft assembly (v2.2) of the wheat genome provided by the International Wheat Genome Sequencing Consortium (IWGSC) and transcribed regions were identifed by mapping a non-redundant set of transcripts to this genomic assembly. Sequencing reads mapping uniquely within these identified transcribed regions were used to determine relative expression profiles. Loci which were differentially expressed in both experimental replicates were designated high-confidence PHYB-regulated and PHYC-regulated genes, respectively. A GTF file is provided detailing the location of the 150,754 loci within the IWGSC pseduomolecules and contig scaffold followed by the longest transcribed sequence mapping to this region. Most, but not all, transcribed sequences are annotated through Ensembl.

2016-06-29 | E-GEOD-79049 | biostudies-arrayexpress

A gene expression microarray for Nicotiana benthamiana based on de novo transcriptome sequence assembly

Project description:Gene expression microarray was designed, based on two recently published versions of the N. benthamiana transcriptome (v.3 and v.5). Based on homology searches and hybridization tests we identified the sense strand in 106,684 transcriptome contigs and used this information to design a Nb-105k microarray on Agilent eArray platform. By the hybridization of N. benthamiana roots vs leaves RNA samples we showed high specificity and sensitivity of the new microarray in detection of differentially expressed transcripts. Agilent microarrays in 2x105k format (two microarrays per slide) were used for hybridization of labeled RNA from leaves vs roots of N. benthamiana plants. Four biological replicates were used for two-color design in a dye-swap manner.

2016-01-08 | E-GEOD-76631 | biostudies-arrayexpress

Transcriptome sequencing on a time series of potato infected with Globodera pallida to explore the sex determination

Project description:We explored the sex determination of Globodera pallida. To do so, we grew cuttings of the potato cultivar Desiree on Gamborg B5 medium supplemented with either 1.5 g/L or 20 g/L sucrose. 14-day-old cuttings were inoculated with 100 G. pallida E400 Rookmaker juveniles. Infected root tissue was harvested at 1, 3, 6, and 9 dpi. Also, a subsample of the ppJ2 was kept for each batch. The experiment contains four time-separated batches. Transcriptome sequencing was performed by BGI Hong Kong. Two samples (B_4.2_1,5; B_4.3_1,5) were not taken along for sequencing because of a failed library prep.

2025-11-25 | E-MTAB-16117 | biostudies-arrayexpress

Proteomics evidences of a systemic response to desiccation in the resurrection plant Haberlea rhodopensis.

Project description:According to the systems biology approach, genomics tells what can happen, transcriptomics what appears to be happening, metabolomics what has happened and proteomics what makes it happen. Thereby, to get a better what makes resurrection plants extremely tolerant to drought, we explored changes in the resurrection proteome and cellular ultrastructure of Haberlea rhodopensis in response to desiccation. Because genomic and proteomic data concerning resurrection plants are limited, particularly for H. rhodopensis, we identified proteins based on previous transcriptomic studies. For the identified proteins, fold changes and differences in transcript levels between fresh and dry plants were analyzed; proteins significantly enriched in various biological processes and metabolic pathways were detected using metabolomic metadata. The results confirmed that the transcription of different genes is regulated as previously described at the proteomic level; new genes were identified in desiccation tolerance, posttranscriptional regulation events, and posttranslational regulation events. We revealed new evidences about organelle and cell preservation, posttranscriptional and posttranslational regulation, photosynthesis, primary metabolism, and phagocytosis in H. rhodopensis. These findings can inform further genomic and evolutionary studies, as well as targeted genetic engineering to improve drought tolerance in crops as a response to climate change.

2022-08-03 | PXD030496 | 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