PRJEB6178 - Acorn Development

Summary
Resource Type
Analysis
Name
PRJEB6178 - Acorn Development
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."

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
PRJEB6178 - Acorn Development
Program Version
Gmap-2018-07-04, SRAtoolkit-2.9.4, SubRead-v1.6.3, TagCleaner-0.16, Trimmomatic-0.38
Date Performed
Monday, September 9, 2019 - 15:20
Data Source
BioSamples
NameTissueTreatmentDescription
ERS445600FruitNot setThis biomaterial: ERS445600, was created for the analysis: PRJEB6178 - Acorn Development
ERS445601FruitNot setThis biomaterial: ERS445601, was created for the analysis: PRJEB6178 - Acorn Development
ERS445602FruitNot setThis biomaterial: ERS445602, was created for the analysis: PRJEB6178 - Acorn Development
ERS445603FruitNot setThis biomaterial: ERS445603, was created for the analysis: PRJEB6178 - Acorn Development
ERS445604FruitNot setThis biomaterial: ERS445604, was created for the analysis: PRJEB6178 - Acorn Development
ERS445605FruitNot setThis biomaterial: ERS445605, was created for the analysis: PRJEB6178 - Acorn Development (normalized)
ERS445606EmbryosNot setThis biomaterial: ERS445606, was created for the analysis: PRJEB6178 - Acorn Development (normalized)