BioProjects

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 ERR490205, ERR490204, ERR490203, ERR490202, ERR490201
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 ERR490206, ERR490207
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 ERR167167, ERR167176, ERR167177, ERR167178, ERR167179, ERR167180, ERR167181, ERR167182, ERR167183, ERR167184, ERR167185, ERR167168, ERR167186, ERR167187, ERR167169, ERR167170, ERR167171, ERR167172, ERR167173, ERR167174, ERR167175
Plant structure development stage Adult trees, 18mo plants
Plant anatomical entity Phloem, Fruit, Roots, Annual stems, Bud, Shoots, Leaves, Xylem, Phellem, Leaves, Seeds, Flowers, Embryos
Type of growth facility Field, Glasshouse, Growth chambers, Greenhouse
Platform 454 GS-FLX
Sequencing Data Description Normalized cDNA libraries
Service Provider Biocant

 

PRJNA392919 - Genome

Investigation unique ID PRJNA392919
Investigation title PRJNA392919 - Genome
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 SRR5986737, SRR5986738, SRR5986739, SRR5986740, SRR5986741
Plant structure development stage 120-150y
Plant anatomical entity Phellem, Xylem, Leaves, Innerbark, Pollen
Type of growth facility field (CO_715:0000163)
Platform Illumina
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 SRR3383083
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 SRR5345606, SRR5345607
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 n/a
Geographic location (country) Portugal:Cercal do Alentejo
External NCBI ID SRR4417263, SRR4417262, SRR4417261, SRR4417260
Plant structure development stage Mature cotyledonary, immature cotyledonary, heart/torpedo, globular
Plant anatomical entity Embryo
Type of growth facility n/a
Platform n/a
Sequencing Data Description n/a
Service Provider n/a

 

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 SRR3119872, 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 SRR1812375, SRR1812376, SRR1812377
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 SRR1609152, SRR1609153
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 SRR1924200, SRR1924199, SRR1924198, SRR1943052
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

 

SRR057583 & SRR057582 - Good/Bad Cork

Investigation unique ID n/a
Investigation title SRR057 - 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 SRR057582, SRR057583
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 SRR1009172, SRR1009171
Plant structure development stage Mature trees, 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