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Series GSE128888 Query DataSets for GSE128888
Status Public on Apr 03, 2019
Title Transcriptome analysis of ARF and Aux/IAA expression during the induction of somatic embryogenesis in Coffea canephora
Organism Coffea canephora
Experiment type Expression profiling by high throughput sequencing
Summary Somatic embryogenesis (SE) is a useful biotechnological tool to study the morpho-physiological, biochemical and molecular processes during the development of Coffea canephora. Plant growth regulators (PGR) play a key role during cell differentiation in SE. The Auxin-response-factor (ARF) and Auxin/Indole-3-acetic acid (Aux/IAA) are fundamental components involved in the signaling of the IAA. The IAA signaling pathway activates or represses the expression of genes responsive to auxins during the embryogenic transition of the somatic cells. The growing development of new generation sequencing technologies (NGS), as well as bioinformatics tools, has allowed us to broaden the landscape of SE study of various plant species and identify the genes directly involved. Analysis of transcriptome expression profiles of the C. canephora genome and the identification of a particular set of differentially expressed genes (DEG) during SE are described in this study. A total of eight ARF and seven Aux/IAA differentially expressed genes were identified during the different stages of the SE induction process. The quantitative expression analysis showed that ARF18 and ARF5 genes are highly expressed after 21 days of the SE induction, while Aux/IAA7 and Aux/IAA12 genes are repressed. The results of this study allow to have a better understanding of the genes involved in auxin signaling pathway as well as their expression profiles during the SE process.
 
Overall design A total of 12 single-end libraries were sequenced via Illumina® NextSeqTM 500 system. Two technical sequencing replicates for each biological sample were conducted corresponding to 14, 9 and 0 days before induction (DBI), and 1, 2 and 21 days after induction (DAI). The 14 DBI sample corresponds to the control.
 
Contributor(s) Quintana-Escobar AO, Nic-Can GI, Galaz-Ávalos RM, Loyola-Vargas VM, Góngora-Castillo EB
Citation(s) 34685847
Submission date Mar 26, 2019
Last update date Nov 03, 2021
Contact name Víctor M. Loyola-Vargas
E-mail(s) vmloyola@cicy.mx
Organization name Centro de Investigación Científica de Yucatán
Department Unidad de Bioquímica y Biología Molecular de Plantas
Lab Laboratorio 24
Street address Calle 43 , No. 130 x 32 y 34
City Mérida
State/province Yucatán
ZIP/Postal code CP 97205
Country Mexico
 
Platforms (1)
GPL26348 Illumina NextSeq 500 (Coffea canephora)
Samples (12)
GSM3688000 14_1_DBI
GSM3688001 14_2_DBI
GSM3688002 9_1_DBI
Relations
BioProject PRJNA529218
SRA SRP189497

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE128888_RAW.tar 2.1 Mb (http)(custom) TAR (of TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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