PRJNA218509 - Good/Bad Cork

BioSamples
Cross Reference
Publication
Summary
BioSamples
NameTissueTreatmentDescription
SRS481410phellogenNot setThis biomaterial: SRS481410, was created for the analysis: PRJNA218509 - Good/Bad Cork
SRS489988phellogenNot setThis biomaterial: SRS489988, was created for the analysis: PRJNA218509 - Good/Bad Cork
Publication
Teixeira RT, Fortes AM, Pinheiro C, Pereira H. Comparison of good- and bad-quality cork: application of high-throughput sequencing of phellogenic tissue.. Journal of experimental botany. 2014 Sep; 65(17):4887-905.
Summary
Name
PRJNA218509 - Good/Bad Cork
Description

"The present work establishes a comparison of phellogenic genes differentially expressed during the development of cork of good and bad quality making use of Roche 454-pyrosequencing."

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
PRJNA218509 - Good/Bad Cork
Program Version
GMAP-2018-07-04, SRAtoolkit-2.9.4, SubRead-v1.6.3, TagCleaner-0.16, Trimmomatic-0.38
Data Source
Source Name
: PRJNA218509
Source URI
: https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA218509