PRJNA309826 - Good/Bad Cork

BioSamples
Cross Reference
Publication
Summary
BioSamples
NameTissueTreatmentDescription
SRR3119876phellogenNot setThis biomaterial: SRR3119876, was created for the analysis: PRJNA309826 - Good/Bad Cork
SRS1262104phellogenNot setThis biomaterial: SRS1262104, was created for the analysis: PRJNA309826 - Good/Bad Cork
Publication
Teixeira RT, Fortes AM, Bai H, Pinheiro C, Pereira H. Transcriptional profiling of cork oak phellogenic cells isolated by laser microdissection.. Planta. 2018 Feb; 247(2):317-338.
Summary
Name
PRJNA309826 - Good/Bad Cork
Description

"Comparative study of cork development using phellogenic cells isolated by laser microdissection. Samples were collected from both high and low quality cork producing trees."

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
PRJNA309826 - 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
: PRJNA309826
Source URI
: https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA309826