PRJEB6178 - Acorn Development (normalized)

BioSamples
Cross Reference
Publication
Summary
BioSamples
NameTissueTreatmentDescription
ERS445605fruitNot setThis biomaterial: ERS445605, was created for the analysis: PRJEB6178 - Acorn Development (normalized)
ERS445606plant embryoNot setThis biomaterial: ERS445606, was created for the analysis: PRJEB6178 - Acorn Development (normalized)
Publication
Miguel A, de Vega-Bartol J, Marum L, Chaves I, Santo T, Leitão J, Varela MC, Miguel CM. Characterization of the cork oak transcriptome dynamics during acorn development.. BMC plant biology. 2015 Jun 25; 15:158.
Summary
Name
PRJEB6178 - Acorn Development (normalized)
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 (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
: PRJEB6178
Source URI
: https://www.ncbi.nlm.nih.gov/bioproject/PRJEB6178