PRJEB3237 – ESTs (normalized)

BioSamples
Cross Reference
Publication
Summary
BioSamples
NameTissueTreatmentDescription
ERS168245xylemNot setThis biomaterial: ERS168245, was created for the analysis: PRJEB3237 – ESTs (normalized)
ERS168246leafNot setThis biomaterial: ERS168246, was created for the analysis: PRJEB3237 – ESTs (normalized)
ERS168247leafNot setThis biomaterial: ERS168247, was created for the analysis: PRJEB3237 – ESTs (normalized)
ERS168248leafNot setThis biomaterial: ERS168248, was created for the analysis: PRJEB3237 – ESTs (normalized)
ERS168249seedNot setThis biomaterial: ERS168249, was created for the analysis: PRJEB3237 – ESTs (normalized)
ERS168250flowerNot setThis biomaterial: ERS168250, was created for the analysis: PRJEB3237 – ESTs (normalized)
ERS168251flowerNot setThis biomaterial: ERS168251, was created for the analysis: PRJEB3237 – ESTs (normalized)
ERS168252embryosNot setThis biomaterial: ERS168252, was created for the analysis: PRJEB3237 – ESTs (normalized)
ERS168253fruitNot setThis biomaterial: ERS168253, was created for the analysis: PRJEB3237 – ESTs (normalized)
ERS168254fruitNot setThis biomaterial: ERS168254, was created for the analysis: PRJEB3237 – ESTs (normalized)

Pages

Publication
Pereira-Leal JB, Abreu IA, Alabaça CS, Almeida MH, Almeida P, Almeida T, Amorim MI, Araújo S, Azevedo H, Badia A, Batista D, Bohn A, Capote T, Carrasquinho I, Chaves I, Coelho AC, Costa MM, Costa R, Cravador A, Egas C, Faro C, Fortes AM, Fortunato AS, Gaspar MJ, Gonçalves S, Graça J, Horta M, Inácio V, Leitão JM, Lino-Neto T, Marum L, Matos J, Mendonça D, Miguel A, Miguel CM, Morais-Cecílio L, Neves I, Nóbrega F, Oliveira MM, Oliveira R, Pais MS, Paiva JA, Paulo OS, Pinheiro M, Raimundo JA, Ramalho JC, Ribeiro AI, Ribeiro T, Rocheta M, Rodrigues AI, Rodrigues JC, Saibo NJ, Santo TE, Santos AM, Sá-Pereira P, Sebastiana M, Simões F, Sobral RS, Tavares R, Teixeira R, Varela C, Veloso MM, Ricardo CP. A comprehensive assessment of the transcriptome of cork oak (Quercus suber) through EST sequencing.. BMC genomics. 2014 May 15; 15:371.
Summary
Name
PRJEB3237 – ESTs (normalized)
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."

FASTQ files were obtained from the NCBI database using the SRAtoolkit-2.9.4. Tags were removed using TagCleaner-0.16 and high quality reads were filtered using Trimmomatic-0.38. Mapping to the reference genome of Q.suber (NCBI Sequence Read Archive SRP111728 (2017)) was performed using Gmap-2018-07-04 and gene expression in TPM (transcripts per million) was calculated using the counts obtained from featureCounts included in SubRead-v1.6.3.
Program, Pipeline, Workflow or Method Name
PRJEB3237 – ESTs (normalized)
Program Version
GMAP-2018-07-04, SRAtoolkit-2.9.4, SubRead-v1.6.3, TagCleaner-0.16, Trimmomatic-0.38
Data Source
Source Name
: PRJEB3237
Source URI
: https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJEB3237