PRJNA347903 - Embryos

BioSamples
Cross Reference
Publication
Summary
BioSamples
NameTissueTreatmentDescription
SRS1739225plant embryoNot setThis biomaterial: SRS1739225, was created for the analysis: PRJNA347903 - Embryos
SRS1739226plant embryoNot setThis biomaterial: SRS1739226, was created for the analysis: PRJNA347903 - Embryos
SRS1739227plant embryoNot setThis biomaterial: SRS1739227, was created for the analysis: PRJNA347903 - Embryos
SRS1739228plant embryoNot setThis biomaterial: SRS1739228, was created for the analysis: PRJNA347903 - Embryos
Publication
Capote, T., Usié, A., Barbosa, P. et al. Transcriptome dynamics of cork oak (Quercus suber) somatic embryogenesis reveals active gene players in transcription regulation and phytohormone homeostasis of embryo development. Tree Genetics & Genomes 15, 52 (2019)
Summary
Name
PRJNA347903 - Embryos
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."

FASTQ files were obtained from the NCBI database using the SRAtoolkit-2.9.4. Mapping to the reference genome of Q.suber (NCBI Sequence Read Archive SRP111728 (2017)) was performed using HISAT2-2.1.0 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
PRJNA347903 - Embryos
Program Version
HISAT2-2.1.0, SRAtoolkit-2.9.4, SubRead-v1.6.3
Data Source
Source Name
: PRJNA347903
Source URI
: https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA347903