PRJNA577816 - Leaves (Heat/Cold)

BioSamples
Cross Reference
Publication
Summary
BioSamples
NameTissueTreatmentDescription
SRS5564252leafCold temperatureThis biomaterial: SRS5564252, was created for the analysis: PRJNA577816 - Leaves (Heat/Cold)
SRS5564253leafCold temperatureThis biomaterial: SRS5564253, was created for the analysis: PRJNA577816 - Leaves (Heat/Cold)
SRS5564254leafControl 25C (cold assay)This biomaterial: SRS5564254, was created for the analysis: PRJNA577816 - Leaves (Heat/Cold)
SRS5564255leafControl 25C (heat assay)This biomaterial: SRS5564255, was created for the analysis: PRJNA577816 - Leaves (Heat/Cold)
SRS5564256leafHeating temperatureThis biomaterial: SRS5564256, was created for the analysis: PRJNA577816 - Leaves (Heat/Cold)
SRS5564257LeafHeating temperatureThis biomaterial: SRS5564257, was created for the analysis: PRJNA577816 - Leaves (Heat/Cold)
Summary
Name
PRJNA577816 - Leaves (Heat/Cold)
Description

"Quercus suber specimens were subjected to cold/heat acclimation and shock. The transcriptome was obtained from leaf samples."

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
PRJNA577816 - Leaves (Heat/Cold)
Program Version
GMAP-2018-07-04, SRAtoolkit-2.9.4, SubRead-v1.6.3, TagCleaner-0.16, Trimmomatic-0.38
Data Source
Source Name
: PRJNA577816
Source URI
: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA577816