Collection of plant gene expression data

Category

Date Issued:

21.10.2024

DOI:

10.24355/dbbs.084-202409160820-0

Language:

English

Type of Resource:

Text

Keywords:

1. Plant genetics

   Typ

   Schlagwort

1. RNA-Sequence

   Typ

   Schlagwort

1. Gene expression

   Typ

   Schlagwort

DDC:

580 Pflanzen (Botanik)

Hosting institution:

02 - Life Sciences

Type:

Text Gene expression data of plant species

Research Object:

Organism

Data Origin:

Other 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). Reference sequences were manually collected from different sources and processed as described below. De novo transcriptome assemblies were generated with Trinity for the following species based on publicly available RNA-seq data: Fagopyrum dibotrys, Myricaria laxiflora, Nepenthes khasiana, Petunia hybrida, Reaumuria songarica, and Tamarix ramosissima.

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. Coding sequences were retrieved from Phytozome, NCBI, and species-specific websites. Alternative transcripts of the same gene were reduced to one representative sequence (longest CDS). For dataset without information about transcript to gene relationships, isoform_purger.py v0.21 (https://github.com/bpucker/PBBtools) was applied. This purging of transcript isoforms reduces the computational costs of downstream analysis steps and contributes to a reduced CO2 footprint. 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. The table '20240914_data_summary.csv' lists the sources of coding sequence data sets that were used as reference for the gene expression analysis. This table also connects the different files belonging to a species with additional metadata.