PRJEB3237 – ESTs (normalized)

Summary
Resource Type
Analysis
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
Date Performed
Tuesday, April 9, 2019 - 12:03
Data Source
BioSamples
NameTissueTreatmentDescription
ERS168265PhloemNot setThis biomaterial: ERS168265, was created for the analysis: PRJEB3237 – ESTs (normalized)
ERS168245XylemNot setThis biomaterial: ERS168245, was created for the analysis: PRJEB3237 – ESTs (normalized)
ERS168246LeavesNot setThis biomaterial: ERS168246, was created for the analysis: PRJEB3237 – ESTs (normalized)
ERS168247LeavesNot setThis biomaterial: ERS168247, was created for the analysis: PRJEB3237 – ESTs (normalized)
ERS168248LeavesNot setThis biomaterial: ERS168248, was created for the analysis: PRJEB3237 – ESTs (normalized)
ERS168249SeedsNot setThis biomaterial: ERS168249, was created for the analysis: PRJEB3237 – ESTs (normalized)
ERS168250Female flowersNot setThis biomaterial: ERS168250, was created for the analysis: PRJEB3237 – ESTs (normalized)
ERS168251Male flowersNot 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)

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