PRJNA309826 - Good/Bad Cork

Summary
Resource Type
Analysis
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
Date Performed
Wednesday, April 10, 2019 - 10:02
Data Source
BioSamples
NameTissueTreatmentDescription
SRS1262104Phellogen (bad quality cork)Not setThis biomaterial: SRS1262104, was created for the analysis: PRJNA309826 - Good/Bad Cork
SRR3119876Phellogen (good quality cork)Not setThis biomaterial: SRR3119876, was created for the analysis: PRJNA309826 - Good/Bad Cork