List of BioProjects present in the portal:
PRJEB6178 - Acorn Development
| Investigation unique ID | PRJEB6178 |
|---|---|
| Investigation title | PRJEB6178 - Acorn Development |
| Investigation description | "In this study, the transcriptome of the cork oak acorn, including the seed, was characterized in five stages of development, from early development to acorn maturation, to identify the dominant processes in each stage and reveal transcripts with important functions in gene expression regulation and response to water." |
| Submission date | 2014-04-30 |
| Associated publication | doi: 10.1186/s12870-015-0534-1 |
| Geographic location (country) | Portugal |
| External NCBI ID | ERS445600, ERS445601, ERS445602, ERS445603, ERS445604 |
| Plant structure development stage | S1, S2, S3 + S4, S5, S8 |
| Plant anatomical entity | Fruit |
| Type of growth facility | field (CO_715:0000163) |
| Platform | 454 GS FLX+ |
| Sequencing Data Description | Non-normalized cDNA |
| Service Provider | Biocant |
PRJEB6178 - Acorn Development (normalized)
| Investigation unique ID | PRJEB6178 |
|---|---|
| Investigation title | PRJEB6178 - Acorn Development (normalized) |
| Investigation description | "In this study, the transcriptome of the cork oak acorn, including the seed, was characterized in five stages of development, from early development to acorn maturation, to identify the dominant processes in each stage and reveal transcripts with important functions in gene expression regulation and response to water." |
| Submission date | 2014-04-30 |
| Associated publication | doi: 10.1186/s12870-015-0534-1 |
| Geographic location (country) | Portugal |
| External NCBI ID | ERS445605, ERS445606 |
| Plant structure development stage | S1-S8 |
| Plant anatomical entity | Fruit |
| Type of growth facility | field (CO_715:0000163) |
| Platform | 454 GS FLX+ |
| Sequencing Data Description | Normalized cDNA |
| Service Provider | Biocant |
PRJEB3237 - ESTs (normalized)
| Investigation unique ID | PRJEB3237 |
|---|---|
| Investigation title | PRJEB3237 - ESTs (normalized) |
| Investigation description | "Over 7 million sequence reads were generated, by pyrosequencing 21 normalized cDNA libraries derived from multiple Quercus suber tissues and organs, developmental stages and physiological conditions." |
| Submission date | 2014-04-01 |
| Associated publication | doi: 10.1186/1471-2164-15-371 |
| Geographic location (country) | Portugal:Tapada da Ajuda, Portugal:Ferreira do Alentejo, Portugal:Braga,, Portugal:Minho, Portugal:Azeitão, Portugal:Porto, Portugal:Santarém, Portugal:Alter do Chão, Portugal:Alentejo, Portugal:Algarve, Portugal:Bragança, Portugal:Lisboa, Portugal:Alcobaça, Andalucia, Tunisia, Morocco, France, Spain |
| External NCBI ID | ERS168245, ERS168246, ERS168247, ERS168248, ERS168249, ERS168250, ERS168251, ERS168252, ERS168253, ERS168254, ERS168255, ERS168256, ERS168257, ERS168258, ERS168259, ERS168260, ERS168261, ERS168262, ERS168263, ERS168264, ERS168265 |
| Plant structure development stage | Adult trees, 4 embryo stages, 7 fruit stages, 18mo plants, bud phases 1,2,3&4 |
| Plant anatomical entity | Xylem, Leaves, Seeds, Flowers, Embryos, Fruit, Roots, Annual stems, Bud, Shoots, Cork, Phloem |
| Type of growth facility | Field, Glasshouse, Growth chambers, Greenhouse |
| Platform | 454 GS-FLX |
| Sequencing Data Description | Normalized cDNA libraries |
| Service Provider | Biocant |
PRJNA392919 - Multi-tissue
| Investigation unique ID | PRJNA392919 |
|---|---|
| Investigation title | PRJNA392919 - Multi-tissue |
| Investigation description | "Project that aimed to unveil and release the genome of the cork oak tree." |
| Submission date | 2018-01-29 |
| Associated publication | doi: 10.1038/sdata.2018.69 |
| Geographic location (country) | Portugal:Montargil |
| External NCBI ID | SRX3142617, SRX3142618, SRX3142619, SRX3142620, SRX3142621 |
| Plant structure development stage | 120-150y |
| Plant anatomical entity | Pollen, Innerbark, Leaves, Xylem, Phellem |
| Type of growth facility | field (CO_715:0000163) |
| Platform | Illumina HiSeq 4000 |
| Sequencing Data Description | Non-normalized RNA-Seq |
| Service Provider | BGI |
PRJNA318475 - Cork (suber x ilex)
| Investigation unique ID | PRJNA318475 |
|---|---|
| Investigation title | PRJNA318475 - Cork (suber x ilex) |
| Investigation description | "Transcriptomic analysis of the cork bark of Quercus suber and Quercus ilex" , 15-20 year-old field-grown trees |
| Submission date | 2016-04-14 |
| Associated publication | doi: 10.1007/s11103-017-0682-9 |
| Geographic location (country) | Spain:La Bisbal |
| External NCBI ID | SRS1396886 |
| Plant structure development stage | 15-20y trees |
| Plant anatomical entity | Phellem |
| Type of growth facility | Field-grown trees (CO_715:0000163) |
| Platform | 454 GS FLX+ |
| Sequencing Data Description | Non-normalized cDNA library |
| Service Provider | n/a |
PRJNA379225 - Buds
| Investigation unique ID | PRJNA379225 |
|---|---|
| Investigation title | PRJNA379225 - Buds |
| Investigation description | "The transcriptome of the cork oak (Quercus suber) was characterized in four stages of bud sprouting development, from bud dormant to bud burst, in order to asses the differences in gene expression over the stages of bud sprouting development." |
| Submission date | 2017-03-15 |
| Associated publication | doi:10.3390/f8120486 |
| Geographic location (country) | Portugal:Monte de Fava (Ermidas do Sado) |
| External NCBI ID | SRS2049704, SRS2049705 |
| Plant structure development stage | Red/open, dormant/swollen |
| Plant anatomical entity | Bud |
| Type of growth facility | Field (CO_715:0000163) |
| Platform | 454 FLX+ |
| Sequencing Data Description | RNA-Seq |
| Service Provider | Biocant |
PRJNA347903 - Embryos
| Investigation unique ID | PRJNA347903 |
|---|---|
| Investigation title | PRJNA347903 - Embryos |
| Investigation description | "The transcriptome of the cork oak somatic embryogenesis was characterized in four stages of embryo development, from globular to mature cotyledonary, to identify relevant genes, namely transcription regulators and genes related with hormone biosynthesis, response, signalling, receptors and metabolism in order to understand the molecular and biochemical events occurring in each specific stage of development." |
| Submission date | n/a |
| Associated publication | doi: 10.1007/s11295-019-1353-6 |
| Geographic location (country) | Portugal:Cercal do Alentejo |
| External NCBI ID | SRS1739225, SRS1739226, SRS1739227, SRS1739228 |
| Plant structure development stage | Globular, heart/torpedo, immature cotyledonary, mature cotyledonary |
| Plant anatomical entity | Embryo |
| Type of growth facility | n/a |
| Platform | Illumina HiSeq 2000 |
| Sequencing Data Description | Non-normalized cDNA |
| Service Provider | BGI |
PRJNA309826 - Good/Bad Cork
| Investigation unique ID | PRJNA309826 |
|---|---|
| Investigation title | PRJNA309826 - Good/Bad Cork |
| Investigation description | "Comparative study of cork development using phellogenic cells isolated by laser microdissection. Samples were collected from both high and low quality cork producing trees." |
| Submission date | 2016-01-26 |
| Associated publication | doi: 10.1007/s00425-017-2786-5 |
| Geographic location (country) | Portugal |
| External NCBI ID | SRS1262104, SRR3119876 |
| Plant structure development stage | 1y branches, young stems |
| Plant anatomical entity | Phellogen |
| Type of growth facility | Field (CO_715:0000163) |
| Platform | 454 GS FLX |
| Sequencing Data Description | Non-normalized cDNA libraries |
| Service Provider | Biocant |
PRJNA275997 - Roots (drought conditions)
| Investigation unique ID | PRJNA275997 |
|---|---|
| Investigation title | PRJNA275997 - Roots (drought conditions) |
| Investigation description | "Sequences from 3 different libraries, concerning 3 different water regiments." - medium drought, severe drought, well watered |
| Submission date | 2015-02-20 |
| Associated publication | doi: 10.3389/fpls.2015.01195 |
| Geographic location (country) | Portugal:Lisbon |
| External NCBI ID | SRS851883, SRS851885, SRS851887 |
| Plant structure development stage | 2mo |
| Plant anatomical entity | Roots |
| Type of growth facility | Growth chamber (CO_715:0000189) |
| Platform | 454 GS FLX+ |
| Sequencing Data Description | Non-normalized cDNA library |
| Service Provider | Biocant |
PRJNA256026 - Flowers
| Investigation unique ID | PRJNA256026 |
|---|---|
| Investigation title | PRJNA256026 - Flowers |
| Investigation description | "The goal of this study is to obtain Next Generating Sequencing-derived flower transcriptome (RNA-seq) of the unisexual flowers of Quercus suber and perform comparative RNAseq analysis to identify determinants of unisexuality." |
| Submission date | 2014-07-24 |
| Associated publication | doi: 10.3389/fpls.2014.00599 |
| Geographic location (country) | Portugal:Lisbon, Portugal:Porto, Portugal:Braga |
| External NCBI ID | SRS666753, SRS716795 |
| Plant structure development stage | Early and late stages of flower development used in pools 1F and 2F (female), and 1M and 2M (male), respectively |
| Plant anatomical entity | Flowers |
| Type of growth facility | Field (CO_715:0000163) |
| Platform | 454 GS FLX+ |
| Sequencing Data Description | Non-normalized cDNA library |
| Service Provider | Biocant |
PRJNA277884 - Roots (P.cinnamomi)
| Investigation unique ID | PRJNA277884 |
|---|---|
| Investigation title | PRJNA277884 - Roots (P.cinnamomi) |
| Investigation description | "The transcriptome analysis of Q. suber directed to genes related to biotic stress caused by Phytophthora cinnamomi infection, the main biotic contributor to the decline disease aims at the characterization of target and regulatory genes that are responsive to the infectious process leading to the understanding of the genetic mechanisms underlying Quercus defence against P. cinnamomi and is an essential prerequisite for the implementation of future control strategies." |
| Submission date | 2015-03-10 |
| Associated publication | n/a |
| Geographic location (country) | Portugal:Algarve, Portugal:Alentejo, Portugal:Lisbon, Spain:Andalusia |
| External NCBI ID | SRS872225, SRS872360, SRS872381, SRS872382 |
| Plant structure development stage | 2weeks; 16mo |
| Plant anatomical entity | Roots |
| Type of growth facility | Growth chamber (CO_715:0000189) |
| Platform | 454 GS FLX |
| Sequencing Data Description | Non-normalized cDNA library |
| Service Provider | Biocant |
SRP002613 - Good/Bad Cork
| Investigation unique ID | n/a |
|---|---|
| Investigation title | SRP002613 - Good/Bad Cork |
| Investigation description | "Besides, the economic importance of cork production and cork manufacturing, little attention has been paid to the molecular mechanisms underlying wood and cork formation as well as cork quality.To overcome this constraint, an international partnership (SuberGene) was established 2008, involving Portuguese and French research institutions and one Producer’s Association organization (FJLF). The main driving force of this partnership is to join efforts and complementary skills to unravel to the molecular mechanisms underlying cork formation and decipher the s tructural polymorphisms and regulation network that determine cork quality." |
| Submission date | 2012-04-15 |
| Associated publication | doi: 10.1186/1753-6561-5-S7-P172 |
| Geographic location (country) | n/a |
| External NCBI ID | SRS083080, SRS083081 |
| Plant structure development stage | n/a |
| Plant anatomical entity | Developing Phellem |
| Type of growth facility | n/a |
| Platform | 454 GS FLX Titanium |
| Sequencing Data Description | Non-normalized cDNA library |
| Service Provider | n/a |
PRJNA218509 - Good/Bad Cork
| Investigation unique ID | PRJNA218509 |
|---|---|
| Investigation title | PRJNA218509 - Good/Bad Cork |
| Investigation description | "The present work establishes a comparison of phellogenic genes differentially expressed during the development of cork of good and bad quality making use of Roche 454-pyrosequencing." |
| Submission date | 2013-09-09 |
| Associated publication | doi: 10.1093/jxb/eru252 |
| Geographic location (country) | Portugal:Alentejo, Portugal:Coruche |
| External NCBI ID | SRS489988, SRS481410 |
| Plant structure development stage | 50-70y |
| Plant anatomical entity | Phellogen |
| Type of growth facility | Field (CO_715:0000163) |
| Platform | 454 GS FLX |
| Sequencing Data Description | Non-normalized cDNA library |
| Service Provider | Biocant |
PRJNA577816 - Leaves (Heat/Cold)
| Investigation unique ID | PRJNA577816 |
|---|---|
| Investigation title | PRJNA577816 - Leaves (Heat/Cold) |
| Investigation description | "Quercus suber specimens were subjected to cold/heat acclimation and shock. The transcriptome was obtained from leaf samples." |
| Submission date | 2019-10-24 |
| Associated publication | n/a |
| Geographic location (country) | Portugal |
| External NCBI ID | SRS5564252, SRS5564253, SRS5564254, SRS5564255, SRS5564256, SRS5564257 |
| Plant structure development stage | 2mo Plants |
| Plant anatomical entity | Leaves |
| Type of growth facility | |
| Platform | 454 GS FLX |
| Sequencing Data Description | Non-normalized cDNA library |
| Service Provider |
PRJEB33874 - Phellem vs. Xylem
| Investigation unique ID | PRJEB33874 |
|---|---|
| Investigation title | PRJEB33874 - Phellem vs. Xylem |
| Investigation description | "Cork cambium (or phellogen) is a secondary meristem, responsible for the formation of phelloderm and phellem/cork, which together compose the periderm. In Quercus suber, the phellogen is active throughout the entire life of the tree, producing a continuous and renewable out-bark of cork. To identify specific candidate genes associated with cork cambium activity and phellem differentiation, we performed a comparative transcriptomic study of Q. suber secondary growth tissues (xylem and phellem), using RNA-seq. The present work provides for the first time a detailed description of all the transcripts identified in phellem tissues. A total of 6013 differentially expressed genes (DEGs) were identified, with 2875 of the transcripts being specifically enriched during the cork formation process versus secondary xylem formation. Furthermore, cork samples originating from the original phellogen (“virgin” cork) and from a traumatic phellogen (“amadia” cork) were also compared. Our results point out to a shortlist of potentially relevant candidate genes regulating phellogen activity and phellem differentiation, including novel genes involved in the suberization process, as well as genes associated to ethylene and jasmonate signalling, and to meristem function. The future functional characterization of some of the identified candidate genes will help to elucidate the molecular mechanisms underlying cork cambium activity and phellem differentiation." |
| Submission date | 2019-08-05 |
| Associated publication | doi: 10.1093/treephys/tpz118 |
| Geographic location (country) | Portugal:Serra de Grândola; Portugal:Benavente |
| External NCBI ID | ERX3494734, ERX3494735, ERX3494736, ERX3494737, ERX3494738, ERX3494739, ERX3494740, ERX3494741, ERX3494742 |
| Plant structure development stage | 20 to 30 yo, secondary growth |
| Plant anatomical entity | Xylem, Phellem |
| Type of growth facility | Field-grown trees (CO_715:0000163) |
| Platform | HiSeq 2500 Illumina |
| Sequencing Data Description | Non-normalized RNA-Seq |
| Service Provider | Fasteris |