Gene expression data sets of selected plant species

Category

Is referenced by:

Conserved amino acid residues and gene expression patterns associated with the substrate preferences of the competing enzymes FLS and DFR Nancy Choudhary [Article / Chapter]. https://doi.org/10.1101/2023.11.05.565693

Date Created:

01.01.2020 - 01.05.2023

Date Issued:

07.11.2023

DOI:

10.24355/dbbs.084-202306231402-0

Language:

English

Type of Resource:

Text

Keywords:

1. Plant genetics

   Typ

   Schlagwort

2. RNA-Seq

   Typ

   Schlagwort

3. Gene expression

   Typ

   Schlagwort

DDC:

572 Biochemie

Type:

Text Gene expression data of plant species

Research Object:

Organism

Data Origin:

Experiment and Measurements RNA-seq data sets were retrieved from the Sequence Read Archive (https://www.ncbi.nlm.nih.gov/sra) via fastq-dump (https://github.com/ncbi/sra-tools).

Used Software:

Editing kallisto (v0.44)

Description of Data Processing:

Gzip-compressed FASTQ files were processed via kallisto v0.44 (https://github.com/pachterlab/kallisto) to quantify gene expression based on annotated coding sequences. The individual count tables produced by kallisto were merged into one count table per species using a Python script (https://github.com/bpucker/CoExp). Samples with a low total number of reads or with a read distribution that does not match RNA-seq expectations were excluded.