PRJNA379225 - Buds

BioSamples
Cross Reference
Publication
Summary
BioSamples
NameTissueTreatmentDescription
SRS2049704budNot setThis biomaterial: SRS2049704, was created for the analysis: PRJNA379225 - Buds
SRS2049705budNot setThis biomaterial: SRS2049705, was created for the analysis: PRJNA379225 - Buds
Publication
Usié, A.; Simões, F.; Barbosa, P.; Meireles, B.; Chaves, I.; Gonçalves, S.; Folgado, A.; Almeida, M.H.; Matos, J.; Ramos, A.M. Comprehensive Analysis of the Cork Oak (Quercus suber) Transcriptome Involved in the Regulation of Bud Sprouting. Forests 2017, 8, 486
Summary
Name
PRJNA379225 - Buds
Description

"The transcriptome of the cork oak (Quercus suber) was characterized in four stages of bud sprouting development, from bud dormant to bud burst, in order to asses the differences in gene expression over the stages of bud sprouting development."

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
PRJNA379225 - Buds
Program Version
GMAP-2018-07-04, SRAtoolkit-2.9.4, SubRead-v1.6.3, TagCleaner-0.16, Trimmomatic-0.38
Data Source
Source Name
: PRJNA379225
Source URI
: https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA379225