Nantaise transcriptome assembly Arias et al. 2020 FASTA file

Resource Type:

File

File Type:

FASTA format

Download:


Download File Name	Available at	Size	MD5
438_2020_1707_MOESM1_ESM.Table_S9.fna.gz	CarrotOmics	8.7MB	e8fb858b4e85ce5ef473fa3874b395a6

Description:

A de novo transcriptome assembly containing 63,164 contigs from supplemental table S9 of the publication. This file has been converted from the Excel format used in the publication to standard FASTA format. For further details see the referenced analysis below.

References:

The following records refer to this file:


Analysis	Nantaise transcriptome assembly Arias et al. 2020 Nantaise transcriptome assembly Arias et al. 2020 blast to DCARv2
Journal Article	A de novo transcriptome analysis revealed that photomorphogenic genes are required for carotenoid synthesis in the dark-grown carrot taproot.
Organism	Daucus carota subsp. sativus

Analysis:


Name	Description
Nantaise transcriptome assembly Arias et al. 2020	Plants of commercially acquired carrot (Daucus carota L.) cultivar Nantaise were harvested 8 weeks after sowing. RNA was sequenced by OMIC Solution (Santiago, Chile) using the Ion Torrent PGM technology (chip P1.1.17) with IonXpress RNA kit (Thermo Fisher Scientific) after library profile analysis using an Agilent 2100 Bioanalyzer (Agilent Technologies, USA). Adapter sequences were removed, and a de novo transcriptome assembly was carried out following CLC Genomics Workbench default parameters including a quimera analysis. The assembly contains 63,164 contigs, from which 18,488 genes are differentially expressed (DEG) between the two experimental conditions light and dark.
Nantaise transcriptome assembly Arias et al. 2020 blast to DCARv2	The assembled sequences from the 2020 transcriptome assembly were mapped to the carrot genome assembly DCARv2 using blastn. Resulting hits were converted to gff3 format for use in the CarrotOmics JBrowse. This file can be downloaded from the link below. Data from this analysis can be viewed in JBrowse here.

Organism:


Name	Common Name	Comment
Daucus carota subsp. sativus	Carrot	For a general overview of carrot, see the Carrot Facts Page

License:


Name	Attribution 4.0 International (CC BY 4.0)
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